6-120860370-T-C

Variant names:

• chr6-120860370-T-C
• rs2251428

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 0.44 in 151,400 control chromosomes in the GnomAD database, including 17,365 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 0.44 (17365 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.678 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: 0.440 AC: 66542 AN: 151282 Hom.: 17317 Cov.: 31

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.440 AC: 66654 AN: 151400 Hom.: 17365 Cov.: 31 AF XY: 0.441 AC XY: 32639 AN XY: 73964

African (AFR) AF: 0.684 AC: 28294 AN: 41338

American (AMR) AF: 0.561 AC: 8528 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1323 AN: 3462

East Asian (EAS) AF: 0.604 AC: 3111 AN: 5152

South Asian (SAS) AF: 0.529 AC: 2540 AN: 4804

European-Finnish (FIN) AF: 0.202 AC: 2129 AN: 10520

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

European-Non Finnish (NFE) AF: 0.289 AC: 19515 AN: 67622

Other (OTH) AF: 0.437 AC: 919 AN: 2102

Alfa AF: 0.458 Hom.: 6372

Bravo AF: 0.477

Asia WGS AF: 0.586 AC: 2028 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.59
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2251428; hg19: chr6-121181516; COSMIC: COSV60276013;