7-97030820-T-G

Variant names:

• chr7-97030820-T-G
• rs6960249
• ENST00000737642.1:n.392+3081T>G

Variant summary

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

The ENST00000737642.1(ENSG00000296253):​n.392+3081T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 152,134 control chromosomes in the GnomAD database, including 9,824 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 0.33 (9824 hom., cov: 33)
• Consequence: ENSG00000296253 ENST00000737642.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.651
• Publications: 4 publications found

Genes affected

ENSG00000296253 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296253	ENST00000737642.1	n.392+3081T>G		intron_variant	Intron 2 of 3
ENSG00000296253	ENST00000737643.1	n.172+3081T>G		intron_variant	Intron 1 of 1
ENSG00000296279	ENST00000737781.1	n.101-3050A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50291 AN: 152016 Hom.: 9829 Cov.: 33

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.331 AC: 50285 AN: 152134 Hom.: 9824 Cov.: 33 AF XY: 0.331 AC XY: 24635 AN XY: 74368

African (AFR) AF: 0.142 AC: 5911 AN: 41516

American (AMR) AF: 0.260 AC: 3974 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1761 AN: 3472

East Asian (EAS) AF: 0.194 AC: 1005 AN: 5180

South Asian (SAS) AF: 0.435 AC: 2092 AN: 4814

European-Finnish (FIN) AF: 0.430 AC: 4548 AN: 10568

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29733 AN: 67986

Other (OTH) AF: 0.350 AC: 740 AN: 2114

Alfa AF: 0.392 Hom.: 6498

Bravo AF: 0.307

Asia WGS AF: 0.314 AC: 1090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	11
DANN	Benign	0.68
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs6960249; hg19: chr7-96660132;