chr4-68524526-A-G

Variant names:

• chr4-68524526-A-G
• rs4492065

Variant summary

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

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 0.83 (48721 hom., cov: 20)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.66
• 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 (EAS) allele frequency at 95% confidence interval = 0.991 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: 0.835 AC: 103395 AN: 123858 Hom.: 48711 Cov.: 20

Gnomad AFR AF: 0.470

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.971

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.997

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.963

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.863

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

GnomAD4 genome AF: 0.835 AC: 103426 AN: 123916 Hom.: 48721 Cov.: 20 AF XY: 0.837 AC XY: 49475 AN XY: 59076

African (AFR) AF: 0.471 AC: 17132 AN: 36392

American (AMR) AF: 0.936 AC: 11239 AN: 12010

Ashkenazi Jewish (ASJ) AF: 0.971 AC: 2846 AN: 2932

East Asian (EAS) AF: 0.998 AC: 1274 AN: 1276

South Asian (SAS) AF: 0.998 AC: 2618 AN: 2624

European-Finnish (FIN) AF: 1.00 AC: 7326 AN: 7328

Middle Eastern (MID) AF: 0.968 AC: 242 AN: 250

European-Non Finnish (NFE) AF: 0.998 AC: 58556 AN: 58678

Other (OTH) AF: 0.864 AC: 1477 AN: 1710

Alfa AF: 0.858 Hom.: 4451

Asia WGS AF: 0.949 AC: 1775 AN: 1872

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.46
DANN	Benign	0.39
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs4492065; hg19: chr4-69390244;