rs76401394

Variant names:

• chr1-173492654-G-T
• rs76401394
• ENST00000779396.1:n.218-212C>A

Variant summary

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

The ENST00000779396.1(ENSG00000301502):​n.218-212C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.048 in 152,278 control chromosomes in the GnomAD database, including 384 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 0.048 (384 hom., cov: 32)
• Consequence: ENSG00000301502 ENST00000779396.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360
• Publications: 0 publications found

Genes affected

ENSG00000301502 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904456	XR_007066738.1	n.365-212C>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301502	ENST00000779396.1	n.218-212C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0480 AC: 7303 AN: 152160 Hom.: 382 Cov.: 32

Gnomad AFR AF: 0.0105

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0335

Gnomad ASJ AF: 0.0337

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.0962

Gnomad FIN AF: 0.0601

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0515

Gnomad OTH AF: 0.0473

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

GnomAD4 genome AF: 0.0480 AC: 7312 AN: 152278 Hom.: 384 Cov.: 32 AF XY: 0.0501 AC XY: 3728 AN XY: 74456

African (AFR) AF: 0.0105 AC: 435 AN: 41578

American (AMR) AF: 0.0335 AC: 512 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0337 AC: 117 AN: 3470

East Asian (EAS) AF: 0.284 AC: 1468 AN: 5174

South Asian (SAS) AF: 0.0967 AC: 466 AN: 4820

European-Finnish (FIN) AF: 0.0601 AC: 638 AN: 10612

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0515 AC: 3504 AN: 68010

Other (OTH) AF: 0.0506 AC: 107 AN: 2114

Alfa AF: 0.0478 Hom.: 45

Bravo AF: 0.0436

Asia WGS AF: 0.198 AC: 689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	6.5
DANN	Benign	0.81
PhyloP100		-0.036

Splicing

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

Other links and lift over

dbSNP: rs76401394; hg19: chr1-173461793;