rs6895261

Variant names:

• chr5-36553974-C-G
• rs6895261

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 0.0407 in 152,288 control chromosomes in the GnomAD database, including 152 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 0.041 (152 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.551
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0501 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: 0.0407 AC: 6188 AN: 152170 Hom.: 152 Cov.: 33

Gnomad AFR AF: 0.0521

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0423

Gnomad ASJ AF: 0.0522

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00664

Gnomad FIN AF: 0.0317

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0395

Gnomad OTH AF: 0.0574

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

GnomAD4 genome AF: 0.0407 AC: 6191 AN: 152288 Hom.: 152 Cov.: 33 AF XY: 0.0398 AC XY: 2963 AN XY: 74458

African (AFR) AF: 0.0520 AC: 2160 AN: 41566

American (AMR) AF: 0.0422 AC: 646 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0522 AC: 181 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5184

South Asian (SAS) AF: 0.00706 AC: 34 AN: 4816

European-Finnish (FIN) AF: 0.0317 AC: 336 AN: 10616

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0396 AC: 2691 AN: 68024

Other (OTH) AF: 0.0572 AC: 121 AN: 2114

Alfa AF: 0.0425 Hom.: 16

Bravo AF: 0.0417

Asia WGS AF: 0.00664 AC: 23 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.1
DANN	Benign	0.65
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs6895261; hg19: chr5-36554076;