rs996544

Variant names:

• chr20-6815572-C-T
• rs996544

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 0.111 in 152,052 control chromosomes in the GnomAD database, including 1,246 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 0.11 (1246 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.920

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.202 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: 0.111 AC: 16807 AN: 151934 Hom.: 1243 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.0549

Gnomad AMR AF: 0.0883

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0450

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.0416

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0703

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.111 AC: 16823 AN: 152052 Hom.: 1246 Cov.: 32 AF XY: 0.111 AC XY: 8223 AN XY: 74330

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.0880

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.0451

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.0416

Gnomad4 NFE AF: 0.0703

Gnomad4 OTH AF: 0.111

Alfa AF: 0.0818 Hom.: 861

Bravo AF: 0.116

Asia WGS AF: 0.138 AC: 478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.43
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs996544; hg19: chr20-6796219;