6-166148224-C-T

Variant names:

• chr6-166148224-C-T
• rs10806845

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 0.415 in 151,998 control chromosomes in the GnomAD database, including 14,346 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 0.41 (14346 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.785
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.506 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: 0.415 AC: 62975 AN: 151882 Hom.: 14335 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.415 AC: 63013 AN: 151998 Hom.: 14346 Cov.: 32 AF XY: 0.411 AC XY: 30539 AN XY: 74292

African (AFR) AF: 0.216 AC: 8961 AN: 41454

American (AMR) AF: 0.497 AC: 7589 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1936 AN: 3468

East Asian (EAS) AF: 0.355 AC: 1834 AN: 5160

South Asian (SAS) AF: 0.510 AC: 2455 AN: 4816

European-Finnish (FIN) AF: 0.382 AC: 4019 AN: 10532

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.511 AC: 34712 AN: 67980

Other (OTH) AF: 0.465 AC: 979 AN: 2104

Alfa AF: 0.480 Hom.: 47851

Bravo AF: 0.416

Asia WGS AF: 0.461 AC: 1604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.7
DANN	Benign	0.32
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs10806845; hg19: chr6-166561712;