rs2654185

Variant names:

• chr17-7280043-A-C
• rs2654185

Your query was ambiguous. Multiple possible variants found:

• chr17-7280043-A-C
• chr17-7280043-A-G
• chr17-7280043-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 0.541 in 152,006 control chromosomes in the GnomAD database, including 23,297 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 0.54 (23297 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.905
• Publications: 31 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.62 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: 0.541 AC: 82174 AN: 151888 Hom.: 23275 Cov.: 32

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.541 AC: 82246 AN: 152006 Hom.: 23297 Cov.: 32 AF XY: 0.544 AC XY: 40380 AN XY: 74276

African (AFR) AF: 0.373 AC: 15462 AN: 41472

American (AMR) AF: 0.557 AC: 8511 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.613 AC: 2130 AN: 3472

East Asian (EAS) AF: 0.378 AC: 1954 AN: 5176

South Asian (SAS) AF: 0.603 AC: 2891 AN: 4798

European-Finnish (FIN) AF: 0.644 AC: 6795 AN: 10546

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.625 AC: 42464 AN: 67958

Other (OTH) AF: 0.595 AC: 1255 AN: 2110

Alfa AF: 0.595 Hom.: 36460

Bravo AF: 0.524

Asia WGS AF: 0.512 AC: 1782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.61
DANN	Benign	0.76
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs2654185; hg19: chr17-7183362;