6-106326155-T-C

Variant names:

• chr6-106326155-T-C
• rs510432

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 0.568 in 152,172 control chromosomes in the GnomAD database, including 26,000 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 0.57 (26000 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162
• Publications: 41 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.759 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: 0.567 AC: 86241 AN: 152054 Hom.: 25935 Cov.: 33

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.568 AC: 86378 AN: 152172 Hom.: 26000 Cov.: 33 AF XY: 0.571 AC XY: 42447 AN XY: 74382

African (AFR) AF: 0.766 AC: 31788 AN: 41500

American (AMR) AF: 0.624 AC: 9546 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1486 AN: 3472

East Asian (EAS) AF: 0.571 AC: 2956 AN: 5178

South Asian (SAS) AF: 0.504 AC: 2436 AN: 4830

European-Finnish (FIN) AF: 0.478 AC: 5060 AN: 10582

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31471 AN: 68006

Other (OTH) AF: 0.528 AC: 1115 AN: 2110

Alfa AF: 0.510 Hom.: 31763

Bravo AF: 0.587

Asia WGS AF: 0.586 AC: 2035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.6
DANN	Benign	0.84
PhyloP100		-0.16
PromoterAI		0.017	Neutral

Splicing

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

Other links and lift over

dbSNP: rs510432; hg19: chr6-106774030;