chr4-68836913-T-G

Variant names:

• chr4-68836913-T-G
• rs6816491

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 0.926 in 152,066 control chromosomes in the GnomAD database, including 65,968 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 0.93 (65968 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.841
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.993 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: 0.926 AC: 140688 AN: 151948 Hom.: 65917 Cov.: 32

Gnomad AFR AF: 0.769

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.971

Gnomad ASJ AF: 0.980

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.961

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.940

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

GnomAD4 genome AF: 0.926 AC: 140798 AN: 152066 Hom.: 65968 Cov.: 32 AF XY: 0.927 AC XY: 68888 AN XY: 74334

African (AFR) AF: 0.769 AC: 31891 AN: 41476

American (AMR) AF: 0.972 AC: 14828 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.980 AC: 3396 AN: 3466

East Asian (EAS) AF: 0.845 AC: 4338 AN: 5134

South Asian (SAS) AF: 0.961 AC: 4628 AN: 4818

European-Finnish (FIN) AF: 1.00 AC: 10618 AN: 10618

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 0.999 AC: 67916 AN: 67976

Other (OTH) AF: 0.941 AC: 1985 AN: 2110

Alfa AF: 0.966 Hom.: 14775

Bravo AF: 0.917

Asia WGS AF: 0.896 AC: 3115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.0
DANN	Benign	0.47
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs6816491; hg19: chr4-69702631;