chr4-146438979-C-T

Variant names:

• chr4-146438979-C-T
• rs191493117
• NM_001029998.6:c.435+3804G>A

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS1

The NM_001029998.6(SLC10A7):​c.435+3804G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000915 in 151,976 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.00091 (0 hom., cov: 32)
• Consequence: SLC10A7 NM_001029998.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108
• Publications: 3 publications found

Genes affected

SLC10A7 (HGNC:23088): (solute carrier family 10 member 7) Enables bile acid transmembrane transporter activity. Involved in several processes, including cellular calcium ion homeostasis; glycoprotein transport; and heparin biosynthetic process. Located in Golgi apparatus and endoplasmic reticulum. Is intrinsic component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC10A7 Gene-Disease associations (from GenCC):

• short stature, amelogenesis imperfecta, and skeletal dysplasia with scoliosis

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.000915 (139/151976) while in subpopulation AFR AF = 0.00275 (114/41488). AF 95% confidence interval is 0.00234. There are 0 homozygotes in GnomAd4. There are 72 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001029998.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC10A7	NM_001029998.6	MANE Select	c.435+3804G>A		intron	N/A	NP_001025169.1
	SLC10A7	NM_001300842.3		c.435+3804G>A		intron	N/A	NP_001287771.1
	SLC10A7	NM_001317816.2		c.396+64870G>A		intron	N/A	NP_001304745.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC10A7	ENST00000335472.12	TSL:1 MANE Select	c.435+3804G>A		intron	N/A	ENSP00000334594.8
	SLC10A7	ENST00000507030.5	TSL:1	c.435+3804G>A		intron	N/A	ENSP00000421275.1
	SLC10A7	ENST00000432059.6	TSL:1	c.396+64870G>A		intron	N/A	ENSP00000411297.2

Frequencies

GnomAD3 genomes AF: 0.000909 AC: 138 AN: 151858 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00273

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000262

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000309

Gnomad OTH AF: 0.00

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.000915 AC: 139 AN: 151976 Hom.: 0 Cov.: 32 AF XY: 0.000969 AC XY: 72 AN XY: 74266

African (AFR) AF: 0.00275 AC: 114 AN: 41488

American (AMR) AF: 0.000262 AC: 4 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5186

South Asian (SAS) AF: 0.00 AC: 0 AN: 4814

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10558

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000309 AC: 21 AN: 67882

Other (OTH) AF: 0.00 AC: 0 AN: 2100

Alfa AF: 0.000763 Hom.: 0

Bravo AF: 0.00109

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.2
DANN	Benign	0.66
PhyloP100		0.11

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs191493117; hg19: chr4-147360131;