6-27869489-T-C

Variant names:

• chr6-27869489-T-C
• rs200953

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 0.123 in 152,042 control chromosomes in the GnomAD database, including 1,323 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 0.12 (1323 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700
• Publications: 29 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.18 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: 0.123 AC: 18713 AN: 151924 Hom.: 1316 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0343

Gnomad EAS AF: 0.0816

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0490

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.123 AC: 18749 AN: 152042 Hom.: 1323 Cov.: 32 AF XY: 0.119 AC XY: 8868 AN XY: 74322

African (AFR) AF: 0.184 AC: 7617 AN: 41444

American (AMR) AF: 0.122 AC: 1861 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0343 AC: 119 AN: 3468

East Asian (EAS) AF: 0.0816 AC: 421 AN: 5162

South Asian (SAS) AF: 0.110 AC: 529 AN: 4808

European-Finnish (FIN) AF: 0.0490 AC: 519 AN: 10600

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7332 AN: 67962

Other (OTH) AF: 0.101 AC: 214 AN: 2112

Alfa AF: 0.118 Hom.: 2647

Bravo AF: 0.130

Asia WGS AF: 0.0980 AC: 340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.64
PhyloP100		-0.070

Splicing

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

Other links and lift over

dbSNP: rs200953; hg19: chr6-27837267;