9-35648953-A-G

Variant names:

• chr9-35648953-A-G
• rs3138083

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 0.407 in 152,074 control chromosomes in the GnomAD database, including 13,359 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 0.41 (13359 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.844 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: 0.407 AC: 61853 AN: 151956 Hom.: 13357 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.866

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.407 AC: 61894 AN: 152074 Hom.: 13359 Cov.: 32 AF XY: 0.410 AC XY: 30449 AN XY: 74338

African (AFR) AF: 0.295 AC: 12238 AN: 41458

American (AMR) AF: 0.413 AC: 6303 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1490 AN: 3470

East Asian (EAS) AF: 0.866 AC: 4480 AN: 5176

South Asian (SAS) AF: 0.550 AC: 2652 AN: 4818

European-Finnish (FIN) AF: 0.413 AC: 4371 AN: 10590

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.427 AC: 29016 AN: 67970

Other (OTH) AF: 0.402 AC: 848 AN: 2112

Alfa AF: 0.424 Hom.: 19063

Bravo AF: 0.404

Asia WGS AF: 0.618 AC: 2150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.2
DANN	Benign	0.55
PhyloP100		-0.073

Splicing

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

Other links and lift over

dbSNP: rs3138083; hg19: chr9-35648950;