rs441859

Variant names:

• chr6-94315304-G-C
• rs441859

Your query was ambiguous. Multiple possible variants found:

• chr6-94315304-G-C
• chr6-94315304-G-T

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 0.133 in 151,958 control chromosomes in the GnomAD database, including 2,131 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 0.13 (2131 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.769
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 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: 0.132 AC: 20084 AN: 151838 Hom.: 2113 Cov.: 31

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.0843

Gnomad ASJ AF: 0.0841

Gnomad EAS AF: 0.0525

Gnomad SAS AF: 0.0911

Gnomad FIN AF: 0.0388

Gnomad MID AF: 0.135

Gnomad NFE AF: 0.0693

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.133 AC: 20137 AN: 151958 Hom.: 2131 Cov.: 31 AF XY: 0.130 AC XY: 9627 AN XY: 74268

African (AFR) AF: 0.298 AC: 12337 AN: 41462

American (AMR) AF: 0.0843 AC: 1287 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0841 AC: 292 AN: 3470

East Asian (EAS) AF: 0.0526 AC: 272 AN: 5170

South Asian (SAS) AF: 0.0909 AC: 439 AN: 4828

European-Finnish (FIN) AF: 0.0388 AC: 411 AN: 10586

Middle Eastern (MID) AF: 0.134 AC: 39 AN: 290

European-Non Finnish (NFE) AF: 0.0693 AC: 4703 AN: 67862

Other (OTH) AF: 0.119 AC: 251 AN: 2108

Alfa AF: 0.0189 Hom.: 10

Bravo AF: 0.143

Asia WGS AF: 0.0980 AC: 345 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.15
DANN	Benign	0.35
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs441859; hg19: chr6-95025022; COSMIC: COSV69413961;