rs751695

chr20-32978321-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;