rs40949

Variant names:

• chr5-148786543-G-A
• rs40949

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 0.412 in 151,948 control chromosomes in the GnomAD database, including 13,636 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 (13636 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.681
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.471 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: 0.412 AC: 62536 AN: 151828 Hom.: 13631 Cov.: 33

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.412 AC: 62553 AN: 151948 Hom.: 13636 Cov.: 33 AF XY: 0.411 AC XY: 30564 AN XY: 74276

African (AFR) AF: 0.278 AC: 11534 AN: 41460

American (AMR) AF: 0.475 AC: 7255 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1903 AN: 3470

East Asian (EAS) AF: 0.319 AC: 1648 AN: 5164

South Asian (SAS) AF: 0.488 AC: 2354 AN: 4828

European-Finnish (FIN) AF: 0.394 AC: 4135 AN: 10506

Middle Eastern (MID) AF: 0.634 AC: 185 AN: 292

European-Non Finnish (NFE) AF: 0.474 AC: 32209 AN: 67942

Other (OTH) AF: 0.448 AC: 947 AN: 2112

Alfa AF: 0.428 Hom.: 1793

Bravo AF: 0.409

Asia WGS AF: 0.401 AC: 1394 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.15
DANN	Benign	0.39
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs40949; hg19: chr5-148166106;