rs6472235

Variant names:

• chr8-65909795-T-G
• rs6472235

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 0.453 in 152,098 control chromosomes in the GnomAD database, including 19,200 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 0.45 (19200 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.888
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.779 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: 0.453 AC: 68871 AN: 151980 Hom.: 19151 Cov.: 32

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.453 AC: 68975 AN: 152098 Hom.: 19200 Cov.: 32 AF XY: 0.444 AC XY: 33035 AN XY: 74376

African (AFR) AF: 0.786 AC: 32593 AN: 41478

American (AMR) AF: 0.382 AC: 5838 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1474 AN: 3464

East Asian (EAS) AF: 0.104 AC: 537 AN: 5182

South Asian (SAS) AF: 0.248 AC: 1194 AN: 4818

European-Finnish (FIN) AF: 0.268 AC: 2836 AN: 10590

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.340 AC: 23121 AN: 67978

Other (OTH) AF: 0.451 AC: 952 AN: 2110

Alfa AF: 0.421 Hom.: 13791

Bravo AF: 0.477

Asia WGS AF: 0.244 AC: 848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.70
DANN	Benign	0.75
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs6472235; hg19: chr8-66822030;