chr6-134167822-T-G

Variant names:

• chr6-134167822-T-G
• rs9402571

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 0.221 in 152,042 control chromosomes in the GnomAD database, including 3,979 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 0.22 (3979 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.271
• Publications: 21 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.394 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: 0.221 AC: 33546 AN: 151922 Hom.: 3969 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.221 AC: 33578 AN: 152042 Hom.: 3979 Cov.: 32 AF XY: 0.226 AC XY: 16832 AN XY: 74322

African (AFR) AF: 0.268 AC: 11120 AN: 41464

American (AMR) AF: 0.158 AC: 2411 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 609 AN: 3464

East Asian (EAS) AF: 0.408 AC: 2111 AN: 5170

South Asian (SAS) AF: 0.251 AC: 1208 AN: 4816

European-Finnish (FIN) AF: 0.243 AC: 2566 AN: 10568

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.188 AC: 12791 AN: 67970

Other (OTH) AF: 0.220 AC: 464 AN: 2112

Alfa AF: 0.192 Hom.: 6018

Bravo AF: 0.216

Asia WGS AF: 0.348 AC: 1206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.8
DANN	Benign	0.70
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs9402571; hg19: chr6-134488960;