6-166172190-A-T

Variant names:

• chr6-166172190-A-T
• rs1001978

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 0.13 in 151,966 control chromosomes in the GnomAD database, including 1,702 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 0.13 (1702 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.398
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.385 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: 0.130 AC: 19699 AN: 151848 Hom.: 1705 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.0820

Gnomad ASJ AF: 0.0761

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.0926

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0773

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.130 AC: 19711 AN: 151966 Hom.: 1702 Cov.: 32 AF XY: 0.133 AC XY: 9897 AN XY: 74274

African (AFR) AF: 0.205 AC: 8511 AN: 41416

American (AMR) AF: 0.0818 AC: 1250 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0761 AC: 264 AN: 3468

East Asian (EAS) AF: 0.400 AC: 2064 AN: 5166

South Asian (SAS) AF: 0.0933 AC: 449 AN: 4812

European-Finnish (FIN) AF: 0.144 AC: 1515 AN: 10550

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0773 AC: 5256 AN: 67964

Other (OTH) AF: 0.122 AC: 257 AN: 2108

Alfa AF: 0.113 Hom.: 138

Bravo AF: 0.132

Asia WGS AF: 0.236 AC: 820 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	13
DANN	Benign	0.93
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs1001978; hg19: chr6-166585678;