17-11035870-T-C

Variant names:

• chr17-11035870-T-C
• rs4791449

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 0.774 in 152,166 control chromosomes in the GnomAD database, including 47,553 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 0.77 (47553 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.94 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: 0.775 AC: 117774 AN: 152048 Hom.: 47542 Cov.: 32

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.845

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.857

Gnomad MID AF: 0.790

Gnomad NFE AF: 0.876

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.774 AC: 117811 AN: 152166 Hom.: 47553 Cov.: 32 AF XY: 0.776 AC XY: 57765 AN XY: 74400

African (AFR) AF: 0.518 AC: 21499 AN: 41484

American (AMR) AF: 0.847 AC: 12946 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.869 AC: 3014 AN: 3470

East Asian (EAS) AF: 0.962 AC: 4967 AN: 5164

South Asian (SAS) AF: 0.842 AC: 4065 AN: 4826

European-Finnish (FIN) AF: 0.857 AC: 9083 AN: 10602

Middle Eastern (MID) AF: 0.777 AC: 227 AN: 292

European-Non Finnish (NFE) AF: 0.876 AC: 59578 AN: 68014

Other (OTH) AF: 0.786 AC: 1661 AN: 2114

Alfa AF: 0.847 Hom.: 232524

Bravo AF: 0.764

Asia WGS AF: 0.875 AC: 3042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.48
PhyloP100		0.068

Splicing

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

Other links and lift over

dbSNP: rs4791449; hg19: chr17-10939187;