17-36058228-T-C

Variant names:

• chr17-36058228-T-C
• rs712040

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 0.24 in 152,170 control chromosomes in the GnomAD database, including 6,641 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 (6641 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.497 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: 0.240 AC: 36438 AN: 152052 Hom.: 6603 Cov.: 32

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.240 AC: 36545 AN: 152170 Hom.: 6641 Cov.: 32 AF XY: 0.242 AC XY: 17991 AN XY: 74398

African (AFR) AF: 0.502 AC: 20841 AN: 41492

American (AMR) AF: 0.256 AC: 3908 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 455 AN: 3466

East Asian (EAS) AF: 0.112 AC: 579 AN: 5182

South Asian (SAS) AF: 0.205 AC: 991 AN: 4826

European-Finnish (FIN) AF: 0.154 AC: 1628 AN: 10596

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7549 AN: 68000

Other (OTH) AF: 0.224 AC: 474 AN: 2112

Alfa AF: 0.230 Hom.: 929

Bravo AF: 0.258

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.23
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs712040; hg19: chr17-34385592;