rs17412370

Variant names:

• chr11-81015321-T-G
• rs17412370

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 0.154 in 152,206 control chromosomes in the GnomAD database, including 2,229 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 0.15 (2229 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.213 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: 0.154 AC: 23412 AN: 152088 Hom.: 2233 Cov.: 32

Gnomad AFR AF: 0.0587

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.00809

Gnomad SAS AF: 0.0981

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.154 AC: 23405 AN: 152206 Hom.: 2229 Cov.: 32 AF XY: 0.151 AC XY: 11203 AN XY: 74412

African (AFR) AF: 0.0587 AC: 2439 AN: 41556

American (AMR) AF: 0.157 AC: 2395 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 688 AN: 3464

East Asian (EAS) AF: 0.00850 AC: 44 AN: 5178

South Asian (SAS) AF: 0.0978 AC: 472 AN: 4828

European-Finnish (FIN) AF: 0.178 AC: 1887 AN: 10604

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.216 AC: 14687 AN: 67990

Other (OTH) AF: 0.182 AC: 385 AN: 2114

Alfa AF: 0.156 Hom.: 1585

Bravo AF: 0.148

Asia WGS AF: 0.0630 AC: 220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.47
PhyloP100		0.097

Splicing

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

Other links and lift over

dbSNP: rs17412370; hg19: chr11-80726364;