rs6545976

Variant names:

• chr2-25171781-G-T
• rs6545976

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 0.164 in 152,100 control chromosomes in the GnomAD database, including 4,396 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 0.16 (4396 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.132
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.441 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: 0.164 AC: 24881 AN: 151982 Hom.: 4384 Cov.: 33

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0743

Gnomad ASJ AF: 0.0804

Gnomad EAS AF: 0.0950

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.0328

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0445

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.164 AC: 24928 AN: 152100 Hom.: 4396 Cov.: 33 AF XY: 0.163 AC XY: 12136 AN XY: 74392

African (AFR) AF: 0.446 AC: 18471 AN: 41424

American (AMR) AF: 0.0741 AC: 1133 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0804 AC: 279 AN: 3470

East Asian (EAS) AF: 0.0946 AC: 490 AN: 5178

South Asian (SAS) AF: 0.170 AC: 817 AN: 4820

European-Finnish (FIN) AF: 0.0328 AC: 348 AN: 10594

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0445 AC: 3024 AN: 68012

Other (OTH) AF: 0.114 AC: 241 AN: 2106

Alfa AF: 0.0768 Hom.: 1852

Bravo AF: 0.177

Asia WGS AF: 0.148 AC: 514 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.4
DANN	Benign	0.19
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs6545976; hg19: chr2-25394650;