6-91408059-T-C

Variant names:

• chr6-91408059-T-C
• rs9351265

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.423 in 152,008 control chromosomes in the GnomAD database, including 14,035 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 0.42 (14035 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.56 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: 0.423 AC: 64224 AN: 151890 Hom.: 14027 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.423 AC: 64242 AN: 152008 Hom.: 14035 Cov.: 32 AF XY: 0.428 AC XY: 31834 AN XY: 74294

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.514

Gnomad4 ASJ AF: 0.510

Gnomad4 EAS AF: 0.577

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.427

Gnomad4 OTH AF: 0.417

Alfa AF: 0.399 Hom.: 4650

Bravo AF: 0.422

Asia WGS AF: 0.483 AC: 1676 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.3
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9351265; hg19: chr6-92117777;