rs441539

Variant names:

• chr6-15764407-T-C
• rs441539

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 0.352 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.327 AC: 13573 AN: 41476

American (AMR) AF: 0.324 AC: 4946 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1458 AN: 3468

East Asian (EAS) AF: 0.206 AC: 1067 AN: 5176

South Asian (SAS) AF: 0.300 AC: 1447 AN: 4820

European-Finnish (FIN) AF: 0.303 AC: 3209 AN: 10580

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26611 AN: 67978

Other (OTH) AF: 0.372 AC: 786 AN: 2112

Alfa AF: 0.380 Hom.: 30428

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
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs441539; hg19: chr6-15764638;