6-103997492-C-T

Variant names:

• chr6-103997492-C-T
• rs9499708

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 0.716 in 151,774 control chromosomes in the GnomAD database, including 40,292 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 0.72 (40292 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.915 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: 0.716 AC: 108523 AN: 151656 Hom.: 40230 Cov.: 31

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.716 AC: 108647 AN: 151774 Hom.: 40292 Cov.: 31 AF XY: 0.718 AC XY: 53250 AN XY: 74170

Gnomad4 AFR AF: 0.923

Gnomad4 AMR AF: 0.706

Gnomad4 ASJ AF: 0.630

Gnomad4 EAS AF: 0.691

Gnomad4 SAS AF: 0.579

Gnomad4 FIN AF: 0.740

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.684

Alfa AF: 0.621 Hom.: 37374

Bravo AF: 0.725

Asia WGS AF: 0.616 AC: 2143 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.14
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9499708; hg19: chr6-104445367;