13-38961638-C-G

Variant names:

• chr13-38961638-C-G
• rs6563655

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 0.226 in 152,034 control chromosomes in the GnomAD database, including 3,992 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 0.23 (3992 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.973
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.235 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: 0.226 AC: 34354 AN: 151916 Hom.: 3983 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.0836

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.226 AC: 34387 AN: 152034 Hom.: 3992 Cov.: 32 AF XY: 0.223 AC XY: 16547 AN XY: 74308

African (AFR) AF: 0.226 AC: 9373 AN: 41494

American (AMR) AF: 0.242 AC: 3687 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1022 AN: 3464

East Asian (EAS) AF: 0.0839 AC: 433 AN: 5158

South Asian (SAS) AF: 0.223 AC: 1074 AN: 4818

European-Finnish (FIN) AF: 0.220 AC: 2326 AN: 10564

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.228 AC: 15478 AN: 67972

Other (OTH) AF: 0.273 AC: 576 AN: 2112

Alfa AF: 0.104 Hom.: 152

Bravo AF: 0.228

Asia WGS AF: 0.216 AC: 750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.3
DANN	Benign	0.73
PhyloP100		0.97

Splicing

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

Other links and lift over

dbSNP: rs6563655; hg19: chr13-39535775;