6-138119701-T-C

Variant names:

• chr6-138119701-T-C
• rs1931867

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 0.446 in 152,060 control chromosomes in the GnomAD database, including 15,584 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 0.45 (15584 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.76 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: 0.446 AC: 67826 AN: 151942 Hom.: 15557 Cov.: 32

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.780

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.446 AC: 67887 AN: 152060 Hom.: 15584 Cov.: 32 AF XY: 0.449 AC XY: 33361 AN XY: 74332

African (AFR) AF: 0.491 AC: 20372 AN: 41460

American (AMR) AF: 0.423 AC: 6473 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1355 AN: 3468

East Asian (EAS) AF: 0.780 AC: 4046 AN: 5186

South Asian (SAS) AF: 0.534 AC: 2573 AN: 4818

European-Finnish (FIN) AF: 0.424 AC: 4475 AN: 10560

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.402 AC: 27350 AN: 67964

Other (OTH) AF: 0.420 AC: 888 AN: 2112

Alfa AF: 0.413 Hom.: 50693

Bravo AF: 0.446

Asia WGS AF: 0.633 AC: 2198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.97
DANN	Benign	0.13
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1931867; hg19: chr6-138440838;