rs2860223

Variant names:

• chr8-133656434-A-G
• rs2860223

Your query was ambiguous. Multiple possible variants found:

• chr8-133656434-A-G
• chr8-133656434-A-T

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 0.349 in 152,106 control chromosomes in the GnomAD database, including 9,699 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 0.35 (9699 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497
• Publications: 6 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 (SAS) allele frequency at 95% confidence interval = 0.501 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: 0.349 AC: 53017 AN: 151986 Hom.: 9693 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.349 AC: 53043 AN: 152106 Hom.: 9699 Cov.: 32 AF XY: 0.356 AC XY: 26444 AN XY: 74334

African (AFR) AF: 0.250 AC: 10395 AN: 41514

American (AMR) AF: 0.402 AC: 6153 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1058 AN: 3470

East Asian (EAS) AF: 0.410 AC: 2119 AN: 5168

South Asian (SAS) AF: 0.518 AC: 2494 AN: 4814

European-Finnish (FIN) AF: 0.422 AC: 4457 AN: 10568

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25182 AN: 67958

Other (OTH) AF: 0.324 AC: 685 AN: 2114

Alfa AF: 0.349 Hom.: 16209

Bravo AF: 0.338

Asia WGS AF: 0.447 AC: 1556 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	0.45
DANN	Benign	0.39
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs2860223; hg19: chr8-134668677; COSMIC: COSV53901212;