chr6-15764407-T-C

Variant names:

• chr6-15764407-T-C
• rs441539

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 0.352 in 152,082 control chromosomes in the GnomAD database, including 9,722 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 0.35 (9722 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.561

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.388 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: 0.352 AC: 53480 AN: 151964 Hom.: 9713 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.352 AC: 53527 AN: 152082 Hom.: 9722 Cov.: 32 AF XY: 0.345 AC XY: 25667 AN XY: 74312

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.372

Alfa AF: 0.386 Hom.: 19249

Bravo AF: 0.352

Asia WGS AF: 0.241 AC: 839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.8
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs441539; hg19: chr6-15764638;