rs4436648

Variant names:

• chr13-22646065-G-A
• rs4436648

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 0.606 in 152,044 control chromosomes in the GnomAD database, including 32,144 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 0.61 (32144 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.781 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: 0.607 AC: 92157 AN: 151926 Hom.: 32143 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.802

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.606 AC: 92160 AN: 152044 Hom.: 32144 Cov.: 32 AF XY: 0.608 AC XY: 45185 AN XY: 74324

African (AFR) AF: 0.229 AC: 9487 AN: 41462

American (AMR) AF: 0.706 AC: 10781 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.786 AC: 2726 AN: 3470

East Asian (EAS) AF: 0.741 AC: 3820 AN: 5156

South Asian (SAS) AF: 0.802 AC: 3866 AN: 4818

European-Finnish (FIN) AF: 0.681 AC: 7197 AN: 10564

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.764 AC: 51957 AN: 67996

Other (OTH) AF: 0.652 AC: 1376 AN: 2112

Alfa AF: 0.721 Hom.: 176897

Bravo AF: 0.593

Asia WGS AF: 0.718 AC: 2496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.65
PhyloP100		0.075

Splicing

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

Other links and lift over

dbSNP: rs4436648; hg19: chr13-23220204;