chr6-99765639-A-G

Variant names:

• chr6-99765639-A-G
• rs4431442

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 0.418 in 152,024 control chromosomes in the GnomAD database, including 15,260 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 0.42 (15260 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.643 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: 0.418 AC: 63513 AN: 151906 Hom.: 15213 Cov.: 32

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.418 AC: 63611 AN: 152024 Hom.: 15260 Cov.: 32 AF XY: 0.416 AC XY: 30938 AN XY: 74318

African (AFR) AF: 0.650 AC: 26919 AN: 41444

American (AMR) AF: 0.375 AC: 5738 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1391 AN: 3468

East Asian (EAS) AF: 0.568 AC: 2942 AN: 5180

South Asian (SAS) AF: 0.510 AC: 2459 AN: 4820

European-Finnish (FIN) AF: 0.261 AC: 2754 AN: 10544

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20180 AN: 67964

Other (OTH) AF: 0.406 AC: 859 AN: 2116

Alfa AF: 0.341 Hom.: 41750

Bravo AF: 0.434

Asia WGS AF: 0.586 AC: 2035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.2
DANN	Benign	0.73
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs4431442; hg19: chr6-100213515;