2-227850659-C-T

Variant names:

• chr2-227850659-C-T
• rs7591163

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 0.712 in 152,082 control chromosomes in the GnomAD database, including 38,926 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 0.71 (38926 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809
• Publications: 15 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 (AMR) allele frequency at 95% confidence interval = 0.758 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: 0.712 AC: 108231 AN: 151964 Hom.: 38925 Cov.: 32

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.712 AC: 108272 AN: 152082 Hom.: 38926 Cov.: 32 AF XY: 0.707 AC XY: 52590 AN XY: 74338

African (AFR) AF: 0.630 AC: 26102 AN: 41456

American (AMR) AF: 0.770 AC: 11763 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.745 AC: 2588 AN: 3472

East Asian (EAS) AF: 0.481 AC: 2491 AN: 5182

South Asian (SAS) AF: 0.716 AC: 3447 AN: 4816

European-Finnish (FIN) AF: 0.715 AC: 7546 AN: 10558

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.764 AC: 51951 AN: 68000

Other (OTH) AF: 0.737 AC: 1556 AN: 2112

Alfa AF: 0.737 Hom.: 82259

Bravo AF: 0.711

Asia WGS AF: 0.596 AC: 2073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.50
DANN	Benign	0.58
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs7591163; hg19: chr2-228715375;