chr8-65939496-G-A

Variant names:

• chr8-65939496-G-A
• rs4601292

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 0.387 in 152,056 control chromosomes in the GnomAD database, including 15,150 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 0.39 (15150 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.387
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.732 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: 0.387 AC: 58740 AN: 151938 Hom.: 15112 Cov.: 32

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.387 AC: 58835 AN: 152056 Hom.: 15150 Cov.: 32 AF XY: 0.380 AC XY: 28234 AN XY: 74314

African (AFR) AF: 0.739 AC: 30649 AN: 41472

American (AMR) AF: 0.294 AC: 4490 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1111 AN: 3466

East Asian (EAS) AF: 0.101 AC: 525 AN: 5176

South Asian (SAS) AF: 0.210 AC: 1013 AN: 4820

European-Finnish (FIN) AF: 0.243 AC: 2564 AN: 10554

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17360 AN: 67982

Other (OTH) AF: 0.372 AC: 784 AN: 2106

Alfa AF: 0.292 Hom.: 33942

Bravo AF: 0.406

Asia WGS AF: 0.223 AC: 776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.7
DANN	Benign	0.65
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs4601292; hg19: chr8-66851731;