chr6-99760562-A-G

Variant names:

• chr6-99760562-A-G
• rs4840086

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 0.337 in 148,956 control chromosomes in the GnomAD database, including 9,920 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 0.34 (9920 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.374
• Publications: 26 publications found

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 (NFE) allele frequency at 95% confidence interval = 0.422 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: 0.337 AC: 50129 AN: 148854 Hom.: 9924 Cov.: 31

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.337 AC: 50134 AN: 148956 Hom.: 9920 Cov.: 31 AF XY: 0.337 AC XY: 24474 AN XY: 72642

African (AFR) AF: 0.115 AC: 4635 AN: 40264

American (AMR) AF: 0.408 AC: 6054 AN: 14834

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1652 AN: 3440

East Asian (EAS) AF: 0.399 AC: 1769 AN: 4438

South Asian (SAS) AF: 0.371 AC: 1601 AN: 4316

European-Finnish (FIN) AF: 0.412 AC: 4330 AN: 10510

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28889 AN: 67872

Other (OTH) AF: 0.380 AC: 790 AN: 2080

Alfa AF: 0.398 Hom.: 36326

Bravo AF: 0.323

Asia WGS AF: 0.326 AC: 1122 AN: 3440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.2
DANN	Benign	0.67
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs4840086; hg19: chr6-100208438;