13-84975601-T-G

Variant names:

• chr13-84975601-T-G
• rs9531686

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 0.497 in 151,756 control chromosomes in the GnomAD database, including 19,293 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 0.50 (19293 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.672 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: 0.497 AC: 75357 AN: 151638 Hom.: 19263 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.497 AC: 75442 AN: 151756 Hom.: 19293 Cov.: 32 AF XY: 0.501 AC XY: 37198 AN XY: 74180

African (AFR) AF: 0.565 AC: 23396 AN: 41414

American (AMR) AF: 0.575 AC: 8745 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1711 AN: 3470

East Asian (EAS) AF: 0.691 AC: 3551 AN: 5136

South Asian (SAS) AF: 0.610 AC: 2945 AN: 4830

European-Finnish (FIN) AF: 0.400 AC: 4221 AN: 10542

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29302 AN: 67838

Other (OTH) AF: 0.491 AC: 1037 AN: 2110

Alfa AF: 0.477 Hom.: 6009

Bravo AF: 0.515

Asia WGS AF: 0.625 AC: 2165 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.38
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs9531686; hg19: chr13-85549736;