6-1261580-T-C

Variant names:

• chr6-1261580-T-C
• rs9378605

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 0.128 in 152,192 control chromosomes in the GnomAD database, including 1,975 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 0.13 (1975 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.466 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: 0.128 AC: 19458 AN: 152074 Hom.: 1965 Cov.: 33

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0834

Gnomad ASJ AF: 0.0778

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.0829

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0657

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.128 AC: 19503 AN: 152192 Hom.: 1975 Cov.: 33 AF XY: 0.133 AC XY: 9867 AN XY: 74420

African (AFR) AF: 0.205 AC: 8514 AN: 41508

American (AMR) AF: 0.0834 AC: 1276 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0778 AC: 270 AN: 3472

East Asian (EAS) AF: 0.481 AC: 2483 AN: 5158

South Asian (SAS) AF: 0.267 AC: 1282 AN: 4808

European-Finnish (FIN) AF: 0.0829 AC: 879 AN: 10608

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0657 AC: 4470 AN: 68014

Other (OTH) AF: 0.123 AC: 259 AN: 2114

Alfa AF: 0.0893 Hom.: 2423

Bravo AF: 0.129

Asia WGS AF: 0.364 AC: 1263 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	0.13
DANN	Benign	0.51
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs9378605; hg19: chr6-1261815;