5-170145929-C-T

Variant names:

• chr5-170145929-C-T
• rs11134616

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 0.71 in 152,030 control chromosomes in the GnomAD database, including 40,304 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 0.71 (40304 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.831 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: 0.710 AC: 107849 AN: 151912 Hom.: 40297 Cov.: 32

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.794

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.837

Gnomad OTH AF: 0.725

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

GnomAD4 genome AF: 0.710 AC: 107892 AN: 152030 Hom.: 40304 Cov.: 32 AF XY: 0.708 AC XY: 52647 AN XY: 74316

African (AFR) AF: 0.460 AC: 19034 AN: 41400

American (AMR) AF: 0.775 AC: 11847 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.796 AC: 2762 AN: 3472

East Asian (EAS) AF: 0.551 AC: 2840 AN: 5156

South Asian (SAS) AF: 0.757 AC: 3648 AN: 4816

European-Finnish (FIN) AF: 0.794 AC: 8409 AN: 10590

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.837 AC: 56921 AN: 67990

Other (OTH) AF: 0.719 AC: 1519 AN: 2114

Alfa AF: 0.791 Hom.: 146288

Bravo AF: 0.697

Asia WGS AF: 0.655 AC: 2277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.42
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs11134616; hg19: chr5-169572933;