chr4-146256189-G-A

Position:

• chr4-146256189-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001029998.6(SLC10A7):​c.*302C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 408,904 control chromosomes in the GnomAD database, including 35,965 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 0.35 (11272 hom., cov: 33)
  • Exomes 𝑓: 0.43 (24693 hom.)
• Consequence: SLC10A7 NM_001029998.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.76

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC10A7	NM_001029998.6	c.*302C>T		3_prime_UTR_variant	12/12	ENST00000335472.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC10A7	ENST00000335472.12	c.*302C>T		3_prime_UTR_variant	12/12	1	NM_001029998.6	P1
SLC10A7	ENST00000432059.6	c.*302C>T		3_prime_UTR_variant	11/11	1
SLC10A7	ENST00000693222.1	c.*302C>T		3_prime_UTR_variant	13/13

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53606 AN: 151986 Hom.: 11272 Cov.: 33

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.347

GnomAD4 exome AF: 0.427 AC: 109661 AN: 256800 Hom.: 24693 Cov.: 0 AF XY: 0.427 AC XY: 58223 AN XY: 136242

Gnomad4 AFR exome AF: 0.100

Gnomad4 AMR exome AF: 0.397

Gnomad4 ASJ exome AF: 0.363

Gnomad4 EAS exome AF: 0.285

Gnomad4 SAS exome AF: 0.402

Gnomad4 FIN exome AF: 0.431

Gnomad4 NFE exome AF: 0.468

Gnomad4 OTH exome AF: 0.415

GnomAD4 genome AF: 0.353 AC: 53618 AN: 152104 Hom.: 11272 Cov.: 33 AF XY: 0.352 AC XY: 26201 AN XY: 74358

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.434

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.346

Alfa AF: 0.440 Hom.: 21872

Bravo AF: 0.338

Asia WGS AF: 0.375 AC: 1300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	12
DANN	Benign	0.75

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

Publications

LitVar

Other links and lift over

dbSNP: rs1057560; hg19: chr4-147177341; COSMIC: COSV53888575; COSMIC: COSV53888575;