chr6-95843924-G-A

Variant names:

• chr6-95843924-G-A
• rs10499007

Variant summary

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

The variant allele was found at a frequency of 0.277 in 151,844 control chromosomes in the GnomAD database, including 6,933 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 0.28 (6933 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250
• Publications: 3 publications found

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 (NFE) allele frequency at 95% confidence interval = 0.366 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

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42069 AN: 151724 Hom.: 6929 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.0268

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.277 AC: 42080 AN: 151844 Hom.: 6933 Cov.: 32 AF XY: 0.277 AC XY: 20524 AN XY: 74218

African (AFR) AF: 0.111 AC: 4585 AN: 41444

American (AMR) AF: 0.358 AC: 5448 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1136 AN: 3466

East Asian (EAS) AF: 0.0267 AC: 138 AN: 5172

South Asian (SAS) AF: 0.260 AC: 1253 AN: 4826

European-Finnish (FIN) AF: 0.332 AC: 3501 AN: 10554

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.369 AC: 25066 AN: 67856

Other (OTH) AF: 0.283 AC: 597 AN: 2106

Alfa AF: 0.346 Hom.: 12606

Bravo AF: 0.269

Asia WGS AF: 0.132 AC: 461 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.64
PhyloP100		-0.025

Splicing

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

Other links and lift over

dbSNP: rs10499007; hg19: chr6-96291800;