rs6938200

Variant names:

• chr6-27263371-A-G
• rs6938200

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 0.166 in 152,156 control chromosomes in the GnomAD database, including 2,276 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 0.17 (2276 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.455
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.196 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: 0.166 AC: 25277 AN: 152038 Hom.: 2274 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.0164

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.166 AC: 25292 AN: 152156 Hom.: 2276 Cov.: 32 AF XY: 0.159 AC XY: 11828 AN XY: 74396

African (AFR) AF: 0.171 AC: 7116 AN: 41500

American (AMR) AF: 0.128 AC: 1955 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 396 AN: 3468

East Asian (EAS) AF: 0.0162 AC: 84 AN: 5182

South Asian (SAS) AF: 0.108 AC: 522 AN: 4826

European-Finnish (FIN) AF: 0.104 AC: 1106 AN: 10600

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13504 AN: 67974

Other (OTH) AF: 0.148 AC: 312 AN: 2112

Alfa AF: 0.187 Hom.: 5311

Bravo AF: 0.167

Asia WGS AF: 0.0780 AC: 271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.6
DANN	Benign	0.32
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs6938200; hg19: chr6-27231150;