rs6140264

Variant names:

• chr20-7395707-G-A
• rs6140264

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 0.153 in 151,954 control chromosomes in the GnomAD database, including 1,956 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 0.15 (1956 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.165
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.278 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: 0.153 AC: 23269 AN: 151836 Hom.: 1948 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.153 AC: 23279 AN: 151954 Hom.: 1956 Cov.: 32 AF XY: 0.158 AC XY: 11725 AN XY: 74242

African (AFR) AF: 0.144 AC: 5963 AN: 41446

American (AMR) AF: 0.191 AC: 2905 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 504 AN: 3468

East Asian (EAS) AF: 0.260 AC: 1336 AN: 5140

South Asian (SAS) AF: 0.291 AC: 1400 AN: 4818

European-Finnish (FIN) AF: 0.147 AC: 1557 AN: 10576

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9089 AN: 67960

Other (OTH) AF: 0.157 AC: 331 AN: 2106

Alfa AF: 0.143 Hom.: 3004

Bravo AF: 0.155

Asia WGS AF: 0.265 AC: 919 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.77
DANN	Benign	0.61
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs6140264; hg19: chr20-7376354;