chr1-173496185-G-A

Variant names:

• chr1-173496185-G-A
• rs7529377
• ENST00000779108.1:n.65+688G>A

Variant summary

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

The ENST00000779108.1(ENSG00000301478):​n.65+688G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,040 control chromosomes in the GnomAD database, including 3,589 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 0.21 (3589 hom., cov: 32)
• Consequence: ENSG00000301478 ENST00000779108.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06
• Publications: 4 publications found

Genes affected

ENSG00000301478 (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 (EAS) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000779108.1. 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
	ENSG00000301478	ENST00000779108.1		n.65+688G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32010 AN: 151922 Hom.: 3579 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.211 AC: 32068 AN: 152040 Hom.: 3589 Cov.: 32 AF XY: 0.209 AC XY: 15512 AN XY: 74306

African (AFR) AF: 0.267 AC: 11044 AN: 41434

American (AMR) AF: 0.188 AC: 2877 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1056 AN: 3468

East Asian (EAS) AF: 0.313 AC: 1618 AN: 5166

South Asian (SAS) AF: 0.117 AC: 566 AN: 4824

European-Finnish (FIN) AF: 0.138 AC: 1457 AN: 10568

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12734 AN: 67992

Other (OTH) AF: 0.209 AC: 440 AN: 2106

Alfa AF: 0.0969 Hom.: 119

Bravo AF: 0.220

Asia WGS AF: 0.210 AC: 729 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	1.5
DANN	Benign	0.78
PhyloP100		-2.1

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: rs7529377;

hg19: chr1-173465324;