rs7584136

Variant names:

• chr2-105216636-A-C
• rs7584136

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 0.42 in 152,090 control chromosomes in the GnomAD database, including 14,180 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 0.42 (14180 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.245
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.499 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: 0.420 AC: 63889 AN: 151972 Hom.: 14179 Cov.: 32

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.420 AC: 63907 AN: 152090 Hom.: 14180 Cov.: 32 AF XY: 0.414 AC XY: 30769 AN XY: 74354

African (AFR) AF: 0.299 AC: 12426 AN: 41490

American (AMR) AF: 0.418 AC: 6388 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2114 AN: 3468

East Asian (EAS) AF: 0.231 AC: 1193 AN: 5162

South Asian (SAS) AF: 0.424 AC: 2040 AN: 4816

European-Finnish (FIN) AF: 0.373 AC: 3945 AN: 10588

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34232 AN: 67948

Other (OTH) AF: 0.438 AC: 924 AN: 2112

Alfa AF: 0.476 Hom.: 67852

Bravo AF: 0.416

Asia WGS AF: 0.294 AC: 1031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.71
DANN	Benign	0.41
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs7584136; hg19: chr2-105833093; COSMIC: COSV60087648;