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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000779396.1. 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
	ENSG00000301502	ENST00000779396.1		n.218-212C>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs76401394;

hg19: chr1-173461793;