chr6-26601298-T-C

Variant names:

• chr6-26601298-T-C
• rs9379897

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 0.111 in 152,014 control chromosomes in the GnomAD database, including 967 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 0.11 (967 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750
• Publications: 29 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.142 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: 0.111 AC: 16788 AN: 151896 Hom.: 964 Cov.: 31

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.0540

Gnomad ASJ AF: 0.0366

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.0780

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.0875

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

GnomAD4 genome AF: 0.111 AC: 16814 AN: 152014 Hom.: 967 Cov.: 31 AF XY: 0.108 AC XY: 8036 AN XY: 74296

African (AFR) AF: 0.144 AC: 5979 AN: 41444

American (AMR) AF: 0.0540 AC: 824 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0366 AC: 127 AN: 3468

East Asian (EAS) AF: 0.100 AC: 518 AN: 5164

South Asian (SAS) AF: 0.151 AC: 726 AN: 4806

European-Finnish (FIN) AF: 0.0780 AC: 824 AN: 10570

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7446 AN: 67974

Other (OTH) AF: 0.0866 AC: 183 AN: 2114

Alfa AF: 0.116 Hom.: 2352

Bravo AF: 0.108

Asia WGS AF: 0.120 AC: 416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.4
DANN	Benign	0.24
PhyloP100		0.075

Splicing

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

Other links and lift over

dbSNP: rs9379897; hg19: chr6-26601526;