rs7561966

Variant names:

• chr2-128746777-A-G
• rs7561966
• ENST00000730281.1:n.773-32083A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-128746777-A-G
• chr2-128746777-A-T

Variant summary

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

The ENST00000730281.1(ENSG00000295469):​n.773-32083A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 151,902 control chromosomes in the GnomAD database, including 6,215 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 0.26 (6215 hom., cov: 32)
• Consequence: ENSG00000295469 ENST00000730281.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.604
• Publications: 5 publications found

Genes affected

ENSG00000295469 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000730281.1. 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
	ENSG00000295469	ENST00000730281.1		n.773-32083A>G		intron	N/A
	ENSG00000295469	ENST00000730282.1		n.744-32083A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40144 AN: 151786 Hom.: 6204 Cov.: 32

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.265 AC: 40199 AN: 151902 Hom.: 6215 Cov.: 32 AF XY: 0.270 AC XY: 20023 AN XY: 74238

African (AFR) AF: 0.425 AC: 17580 AN: 41384

American (AMR) AF: 0.242 AC: 3703 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1001 AN: 3466

East Asian (EAS) AF: 0.318 AC: 1636 AN: 5146

South Asian (SAS) AF: 0.231 AC: 1114 AN: 4814

European-Finnish (FIN) AF: 0.235 AC: 2479 AN: 10562

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11844 AN: 67944

Other (OTH) AF: 0.253 AC: 532 AN: 2102

Alfa AF: 0.284 Hom.: 2619

Bravo AF: 0.274

Asia WGS AF: 0.275 AC: 957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.2
DANN	Benign	0.49
PhyloP100		-0.60

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: rs7561966;

hg19: chr2-129504351;