4-146522385-C-T

Variant names:

• chr4-146522385-C-T
• rs41398848
• ENST00000692741.3:n.817C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000692741.3(ENSG00000288998):​n.817C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 152,014 control chromosomes in the GnomAD database, including 5,102 homozygotes. 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 0.25 (5102 hom., cov: 32)
• Consequence: ENSG00000288998 ENST00000692741.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.543
• Publications: 3 publications found

Genes affected

ENSG00000288998 (HGNC:):

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000692741.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288998	ENST00000692741.3		n.817C>T		non_coding_transcript_exon	Exon 1 of 1
	SLC10A7	ENST00000685433.1		n.-13G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37684 AN: 151896 Hom.: 5094 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.248 AC: 37712 AN: 152014 Hom.: 5102 Cov.: 32 AF XY: 0.251 AC XY: 18658 AN XY: 74268

African (AFR) AF: 0.159 AC: 6606 AN: 41480

American (AMR) AF: 0.356 AC: 5441 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 483 AN: 3468

East Asian (EAS) AF: 0.378 AC: 1936 AN: 5120

South Asian (SAS) AF: 0.189 AC: 911 AN: 4814

European-Finnish (FIN) AF: 0.304 AC: 3205 AN: 10548

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18372 AN: 67978

Other (OTH) AF: 0.248 AC: 524 AN: 2112

Alfa AF: 0.261 Hom.: 1204

Bravo AF: 0.250

Asia WGS AF: 0.292 AC: 1010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	9.9
DANN	Benign	0.87
PhyloP100		-0.54
PromoterAI		-0.31	Neutral

Splicing

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

Other links and lift over

dbSNP: rs41398848; hg19: chr4-147443537;