rs10521277

Variant names:

• chr17-14619634-G-A
• rs10521277

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 0.235 in 152,008 control chromosomes in the GnomAD database, including 4,232 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 0.24 (4232 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.3 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: 0.236 AC: 35771 AN: 151890 Hom.: 4227 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.235 AC: 35789 AN: 152008 Hom.: 4232 Cov.: 32 AF XY: 0.237 AC XY: 17604 AN XY: 74284

African (AFR) AF: 0.214 AC: 8876 AN: 41458

American (AMR) AF: 0.251 AC: 3828 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 718 AN: 3468

East Asian (EAS) AF: 0.313 AC: 1609 AN: 5148

South Asian (SAS) AF: 0.288 AC: 1383 AN: 4806

European-Finnish (FIN) AF: 0.229 AC: 2415 AN: 10568

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16136 AN: 67978

Other (OTH) AF: 0.241 AC: 509 AN: 2112

Alfa AF: 0.238 Hom.: 3815

Bravo AF: 0.237

Asia WGS AF: 0.301 AC: 1043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.1
DANN	Benign	0.55
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs10521277; hg19: chr17-14522951;