rs7761965

Variant names:

• chr6-31305718-G-A
• rs7761965
• ENST00000755297.1:n.32+34612G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-31305718-G-A
• chr6-31305718-G-T

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.32+34612G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 151,184 control chromosomes in the GnomAD database, including 1,694 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 0.14 (1694 hom., cov: 31)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.891
• Publications: 24 publications found

Genes affected

ENSG00000298396 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755297.1. 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
	ENSG00000298396	ENST00000755297.1		n.32+34612G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20450 AN: 151066 Hom.: 1688 Cov.: 31

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0571

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.0867

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.135 AC: 20481 AN: 151184 Hom.: 1694 Cov.: 31 AF XY: 0.142 AC XY: 10507 AN XY: 73788

African (AFR) AF: 0.110 AC: 4526 AN: 41084

American (AMR) AF: 0.222 AC: 3357 AN: 15132

Ashkenazi Jewish (ASJ) AF: 0.0867 AC: 301 AN: 3472

East Asian (EAS) AF: 0.358 AC: 1844 AN: 5158

South Asian (SAS) AF: 0.240 AC: 1143 AN: 4768

European-Finnish (FIN) AF: 0.140 AC: 1457 AN: 10396

Middle Eastern (MID) AF: 0.188 AC: 55 AN: 292

European-Non Finnish (NFE) AF: 0.109 AC: 7413 AN: 67872

Other (OTH) AF: 0.159 AC: 333 AN: 2100

Alfa AF: 0.116 Hom.: 3887

Bravo AF: 0.139

Asia WGS AF: 0.320 AC: 1109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.1
DANN	Benign	0.45
PhyloP100		-0.89

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: rs7761965;

hg19: chr6-31273495;