rs6071980

Variant names:

• chr20-40239936-T-C
• rs6071980

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 0.157 in 152,216 control chromosomes in the GnomAD database, including 2,012 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 0.16 (2012 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.221 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: 0.157 AC: 23904 AN: 152100 Hom.: 2001 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.157 AC: 23946 AN: 152216 Hom.: 2012 Cov.: 32 AF XY: 0.157 AC XY: 11695 AN XY: 74412

African (AFR) AF: 0.164 AC: 6794 AN: 41534

American (AMR) AF: 0.216 AC: 3298 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 453 AN: 3470

East Asian (EAS) AF: 0.232 AC: 1198 AN: 5174

South Asian (SAS) AF: 0.195 AC: 942 AN: 4820

European-Finnish (FIN) AF: 0.106 AC: 1119 AN: 10590

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.141 AC: 9612 AN: 68022

Other (OTH) AF: 0.174 AC: 368 AN: 2116

Alfa AF: 0.152 Hom.: 5293

Bravo AF: 0.167

Asia WGS AF: 0.226 AC: 785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	0.14
DANN	Benign	0.88
PhyloP100		0.032

Splicing

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

Other links and lift over

dbSNP: rs6071980; hg19: chr20-38868576;