6-119939824-T-C

Variant names:

• chr6-119939824-T-C
• rs1074195

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 0.427 in 151,772 control chromosomes in the GnomAD database, including 14,279 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 0.43 (14279 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.263
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.736 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: 0.427 AC: 64747 AN: 151654 Hom.: 14270 Cov.: 31

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.427 AC: 64792 AN: 151772 Hom.: 14279 Cov.: 31 AF XY: 0.426 AC XY: 31632 AN XY: 74182

African (AFR) AF: 0.451 AC: 18681 AN: 41400

American (AMR) AF: 0.367 AC: 5594 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1417 AN: 3460

East Asian (EAS) AF: 0.755 AC: 3889 AN: 5148

South Asian (SAS) AF: 0.473 AC: 2275 AN: 4814

European-Finnish (FIN) AF: 0.417 AC: 4383 AN: 10514

Middle Eastern (MID) AF: 0.459 AC: 134 AN: 292

European-Non Finnish (NFE) AF: 0.400 AC: 27125 AN: 67868

Other (OTH) AF: 0.439 AC: 927 AN: 2110

Alfa AF: 0.417 Hom.: 1674

Bravo AF: 0.430

Asia WGS AF: 0.601 AC: 2083 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	4.1
DANN	Benign	0.87
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs1074195; hg19: chr6-120260970; COSMIC: COSV60273591;