rs751695

Variant names:

• chr20-32978321-T-C
• rs751695

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.549 in 151,868 control chromosomes in the GnomAD database, including 23,770 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 0.55 (23770 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.938

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.634 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: 0.549 AC: 83352 AN: 151750 Hom.: 23743 Cov.: 31

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.0757

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.549 AC: 83426 AN: 151868 Hom.: 23770 Cov.: 31 AF XY: 0.547 AC XY: 40626 AN XY: 74206

Gnomad4 AFR AF: 0.641

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.555

Gnomad4 EAS AF: 0.0757

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.585

Gnomad4 NFE AF: 0.538

Gnomad4 OTH AF: 0.568

Alfa AF: 0.534 Hom.: 44729

Bravo AF: 0.547

Asia WGS AF: 0.297 AC: 1035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs751695; hg19: chr20-31566127;