6-40697676-C-T

Position:

• chr6-40697676-C-T

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 0.264 in 152,108 control chromosomes in the GnomAD database, including 5,997 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 0.26 (5997 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.951

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40110 AN: 151990 Hom.: 5984 Cov.: 33

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.264 AC: 40138 AN: 152108 Hom.: 5997 Cov.: 33 AF XY: 0.265 AC XY: 19700 AN XY: 74350

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.398

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.279

Alfa AF: 0.209 Hom.: 6396

Bravo AF: 0.272

Asia WGS AF: 0.356 AC: 1242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	11
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6931798; hg19: chr6-40665415;