1-232916595-A-G

Variant names:

• chr1-232916595-A-G
• rs2224402
• ENST00000795545.1:n.77+3540A>G

Variant summary

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

The ENST00000795545.1(ENSG00000303556):​n.77+3540A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 151,956 control chromosomes in the GnomAD database, including 26,105 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 0.55 (26105 hom., cov: 32)
• Consequence: ENSG00000303556 ENST00000795545.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800
• Publications: 6 publications found

Genes affected

ENSG00000303556 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000795545.1. 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
	ENSG00000303556	ENST00000795545.1		n.77+3540A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83138 AN: 151838 Hom.: 26110 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.547 AC: 83134 AN: 151956 Hom.: 26105 Cov.: 32 AF XY: 0.548 AC XY: 40697 AN XY: 74246

African (AFR) AF: 0.214 AC: 8874 AN: 41464

American (AMR) AF: 0.591 AC: 9024 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.723 AC: 2506 AN: 3464

East Asian (EAS) AF: 0.622 AC: 3204 AN: 5152

South Asian (SAS) AF: 0.623 AC: 2996 AN: 4812

European-Finnish (FIN) AF: 0.654 AC: 6874 AN: 10514

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.700 AC: 47567 AN: 67978

Other (OTH) AF: 0.606 AC: 1277 AN: 2108

Alfa AF: 0.649 Hom.: 64188

Bravo AF: 0.522

Asia WGS AF: 0.610 AC: 2124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.39
PhyloP100		-0.0080

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: rs2224402;

hg19: chr1-233052341;