rs1507939

Variant names:

• chr4-115244216-C-T
• rs1507939

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 0.345 in 151,282 control chromosomes in the GnomAD database, including 11,111 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 0.35 (11111 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52249 AN: 151164 Hom.: 11105 Cov.: 31

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.345 AC: 52264 AN: 151282 Hom.: 11111 Cov.: 31 AF XY: 0.337 AC XY: 24929 AN XY: 73922

African (AFR) AF: 0.109 AC: 4512 AN: 41390

American (AMR) AF: 0.411 AC: 6209 AN: 15122

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1009 AN: 3466

East Asian (EAS) AF: 0.188 AC: 970 AN: 5154

South Asian (SAS) AF: 0.235 AC: 1129 AN: 4806

European-Finnish (FIN) AF: 0.388 AC: 4052 AN: 10434

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.489 AC: 33089 AN: 67608

Other (OTH) AF: 0.360 AC: 757 AN: 2100

Alfa AF: 0.442 Hom.: 8320

Bravo AF: 0.343

Asia WGS AF: 0.209 AC: 721 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.0
DANN	Benign	0.28
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1507939; hg19: chr4-116165372;