5-150413894-C-T

Variant names:

• chr5-150413894-C-T
• rs1560661

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 0.611 in 152,072 control chromosomes in the GnomAD database, including 29,070 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 0.61 (29070 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.519
• Publications: 8 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 (AFR) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92803 AN: 151954 Hom.: 29021 Cov.: 32

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.611 AC: 92911 AN: 152072 Hom.: 29070 Cov.: 32 AF XY: 0.608 AC XY: 45182 AN XY: 74324

African (AFR) AF: 0.743 AC: 30809 AN: 41470

American (AMR) AF: 0.493 AC: 7538 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1964 AN: 3468

East Asian (EAS) AF: 0.575 AC: 2977 AN: 5178

South Asian (SAS) AF: 0.687 AC: 3307 AN: 4812

European-Finnish (FIN) AF: 0.491 AC: 5187 AN: 10556

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.575 AC: 39099 AN: 67988

Other (OTH) AF: 0.586 AC: 1234 AN: 2106

Alfa AF: 0.583 Hom.: 39129

Bravo AF: 0.614

Asia WGS AF: 0.611 AC: 2128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.30
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs1560661; hg19: chr5-149793457;