rs957334

Variant names:

• chr1-94563425-A-C
• rs957334
• ENST00000782778.1:n.153A>C

Variant summary

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

The ENST00000782778.1(ENSG00000301906):​n.153A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 151,982 control chromosomes in the GnomAD database, including 19,862 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 0.51 (19862 hom., cov: 32)
• Consequence: ENSG00000301906 ENST00000782778.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610
• Publications: 1 publications found

Genes affected

ENSG00000301906 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000782778.1. 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
	ENSG00000301906	ENST00000782778.1		n.153A>C		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000301906	ENST00000782779.1		n.142A>C		non_coding_transcript_exon	Exon 1 of 4

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77439 AN: 151864 Hom.: 19837 Cov.: 32

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.510 AC: 77525 AN: 151982 Hom.: 19862 Cov.: 32 AF XY: 0.509 AC XY: 37817 AN XY: 74256

African (AFR) AF: 0.560 AC: 23197 AN: 41436

American (AMR) AF: 0.548 AC: 8372 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2070 AN: 3470

East Asian (EAS) AF: 0.510 AC: 2624 AN: 5150

South Asian (SAS) AF: 0.427 AC: 2062 AN: 4824

European-Finnish (FIN) AF: 0.430 AC: 4542 AN: 10566

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.486 AC: 33048 AN: 67958

Other (OTH) AF: 0.526 AC: 1109 AN: 2110

Alfa AF: 0.488 Hom.: 9455

Bravo AF: 0.520

Asia WGS AF: 0.479 AC: 1665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.5
DANN	Benign	0.39
PhyloP100		0.061

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: rs957334;

hg19: chr1-95028981;