rs87938

Variant names:

• chr3-41096181-A-G
• rs87938
• ENST00000808368.1:n.394+369T>C

Your query was ambiguous. Multiple possible variants found:

• chr3-41096181-A-G
• chr3-41096181-A-T

Variant summary

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

The ENST00000808368.1(ENSG00000305067):​n.394+369T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 151,958 control chromosomes in the GnomAD database, including 28,342 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 0.60 (28342 hom., cov: 31)
• Consequence: ENSG00000305067 ENST00000808368.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143
• Publications: 30 publications found

Genes affected

ENSG00000305067 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305067	ENST00000808368.1	n.394+369T>C		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90345 AN: 151840 Hom.: 28296 Cov.: 31

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.595 AC: 90449 AN: 151958 Hom.: 28342 Cov.: 31 AF XY: 0.586 AC XY: 43553 AN XY: 74272

African (AFR) AF: 0.780 AC: 32317 AN: 41454

American (AMR) AF: 0.480 AC: 7334 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1459 AN: 3470

East Asian (EAS) AF: 0.362 AC: 1861 AN: 5144

South Asian (SAS) AF: 0.342 AC: 1649 AN: 4820

European-Finnish (FIN) AF: 0.593 AC: 6256 AN: 10556

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.556 AC: 37751 AN: 67922

Other (OTH) AF: 0.578 AC: 1217 AN: 2106

Alfa AF: 0.558 Hom.: 76206

Bravo AF: 0.599

Asia WGS AF: 0.397 AC: 1385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	9.4
DANN	Benign	0.53
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs87938; hg19: chr3-41137672;