chr7-96717788-G-A

Variant names:

• chr7-96717788-G-A
• rs10808101
• ENST00000796677.1:n.158+2995G>A

Variant summary

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

The ENST00000796677.1(ENSG00000303709):​n.158+2995G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 151,890 control chromosomes in the GnomAD database, including 2,157 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 0.17 (2157 hom., cov: 32)
• Consequence: ENSG00000303709 ENST00000796677.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• Publications: 5 publications found

Genes affected

ENSG00000303709 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000796677.1. 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
	ENSG00000303709	ENST00000796677.1		n.158+2995G>A		intron	N/A
	ENSG00000303709	ENST00000796678.1		n.498+2995G>A		intron	N/A
	ENSG00000303709	ENST00000796679.1		n.54-6024G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25304 AN: 151772 Hom.: 2153 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.167 AC: 25333 AN: 151890 Hom.: 2157 Cov.: 32 AF XY: 0.171 AC XY: 12671 AN XY: 74228

African (AFR) AF: 0.136 AC: 5639 AN: 41460

American (AMR) AF: 0.173 AC: 2640 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 515 AN: 3472

East Asian (EAS) AF: 0.189 AC: 981 AN: 5180

South Asian (SAS) AF: 0.209 AC: 1008 AN: 4812

European-Finnish (FIN) AF: 0.225 AC: 2373 AN: 10538

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11694 AN: 67876

Other (OTH) AF: 0.168 AC: 354 AN: 2106

Alfa AF: 0.173 Hom.: 1211

Bravo AF: 0.161

Asia WGS AF: 0.234 AC: 811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.95
DANN	Benign	0.34
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs10808101; hg19: chr7-96347100;