rs12671838

Variant names:

• chr7-37900722-G-A
• rs12671838
• ENST00000476620.1:c.-38+43377G>A

Variant summary

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

The ENST00000476620.1(ENSG00000290149):​c.-38+43377G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0876 in 152,152 control chromosomes in the GnomAD database, including 978 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 0.088 (978 hom., cov: 32)
• Consequence: ENSG00000290149 ENST00000476620.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196
• Publications: 5 publications found

Genes affected

ENSG00000290149 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000476620.1. 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
	ENSG00000290149	ENST00000476620.1	TSL:4	c.-38+43377G>A		intron	N/A	ENSP00000425858.1	D6RIH7

Frequencies

GnomAD3 genomes AF: 0.0874 AC: 13293 AN: 152032 Hom.: 963 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.0784

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.0456

Gnomad MID AF: 0.0605

Gnomad NFE AF: 0.0350

Gnomad OTH AF: 0.0883

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

GnomAD4 genome AF: 0.0876 AC: 13324 AN: 152152 Hom.: 978 Cov.: 32 AF XY: 0.0936 AC XY: 6964 AN XY: 74386

African (AFR) AF: 0.136 AC: 5641 AN: 41492

American (AMR) AF: 0.218 AC: 3324 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0239 AC: 83 AN: 3468

East Asian (EAS) AF: 0.0782 AC: 403 AN: 5154

South Asian (SAS) AF: 0.164 AC: 790 AN: 4820

European-Finnish (FIN) AF: 0.0456 AC: 484 AN: 10610

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0350 AC: 2378 AN: 68012

Other (OTH) AF: 0.0874 AC: 185 AN: 2116

Alfa AF: 0.0605 Hom.: 795

Bravo AF: 0.0997

Asia WGS AF: 0.141 AC: 491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.5
DANN	Benign	0.73
PhyloP100		0.20
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs12671838; hg19: chr7-37940324;