rs4505549

Variant names:

• chr2-195423412-T-C
• rs4505549

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 0.466 in 151,914 control chromosomes in the GnomAD database, including 19,861 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 0.47 (19861 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.351
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.613 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: 0.467 AC: 70844 AN: 151796 Hom.: 19866 Cov.: 31

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.466 AC: 70830 AN: 151914 Hom.: 19861 Cov.: 31 AF XY: 0.470 AC XY: 34856 AN XY: 74218

African (AFR) AF: 0.145 AC: 6022 AN: 41466

American (AMR) AF: 0.487 AC: 7418 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2160 AN: 3472

East Asian (EAS) AF: 0.321 AC: 1658 AN: 5162

South Asian (SAS) AF: 0.570 AC: 2739 AN: 4808

European-Finnish (FIN) AF: 0.666 AC: 7020 AN: 10536

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.618 AC: 41976 AN: 67920

Other (OTH) AF: 0.487 AC: 1027 AN: 2108

Alfa AF: 0.567 Hom.: 42937

Bravo AF: 0.435

Asia WGS AF: 0.426 AC: 1482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.1
DANN	Benign	0.45
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs4505549; hg19: chr2-196288136;