chr7-128217273-A-G

Variant names:

• chr7-128217273-A-G
• rs6947095
• ENST00000710955.1:n.836-6760A>G

Variant summary

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

The ENST00000710955.1(ENSG00000292309):​n.836-6760A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.836 in 152,230 control chromosomes in the GnomAD database, including 53,376 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 0.84 (53376 hom., cov: 33)
• Consequence: ENSG00000292309 ENST00000710955.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0870
• Publications: 3 publications found

Genes affected

ENSG00000292309 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.881 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000710955.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000292309	ENST00000710955.1		n.836-6760A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.836 AC: 127185 AN: 152112 Hom.: 53335 Cov.: 33

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.843

Gnomad FIN AF: 0.851

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.817

Gnomad OTH AF: 0.838

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

GnomAD4 genome AF: 0.836 AC: 127282 AN: 152230 Hom.: 53376 Cov.: 33 AF XY: 0.836 AC XY: 62237 AN XY: 74422

African (AFR) AF: 0.887 AC: 36827 AN: 41520

American (AMR) AF: 0.756 AC: 11559 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.812 AC: 2816 AN: 3470

East Asian (EAS) AF: 0.902 AC: 4673 AN: 5178

South Asian (SAS) AF: 0.844 AC: 4072 AN: 4824

European-Finnish (FIN) AF: 0.851 AC: 9023 AN: 10606

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.817 AC: 55582 AN: 68026

Other (OTH) AF: 0.839 AC: 1774 AN: 2114

Alfa AF: 0.820 Hom.: 133260

Bravo AF: 0.829

Asia WGS AF: 0.874 AC: 3038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.9
DANN	Benign	0.44
PhyloP100		0.087

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6947095; hg19: chr7-127857326;