chr5-178999318-T-C

Variant names:

• chr5-178999318-T-C
• rs11249608

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 0.624 in 150,550 control chromosomes in the GnomAD database, including 29,898 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 0.62 (29898 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.691 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: 0.624 AC: 93890 AN: 150442 Hom.: 29878 Cov.: 26

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.691

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.624 AC: 93947 AN: 150550 Hom.: 29898 Cov.: 26 AF XY: 0.622 AC XY: 45634 AN XY: 73364

African (AFR) AF: 0.497 AC: 20411 AN: 41050

American (AMR) AF: 0.648 AC: 9783 AN: 15104

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2456 AN: 3464

East Asian (EAS) AF: 0.482 AC: 2392 AN: 4964

South Asian (SAS) AF: 0.604 AC: 2873 AN: 4754

European-Finnish (FIN) AF: 0.656 AC: 6727 AN: 10248

Middle Eastern (MID) AF: 0.692 AC: 202 AN: 292

European-Non Finnish (NFE) AF: 0.696 AC: 47130 AN: 67700

Other (OTH) AF: 0.617 AC: 1278 AN: 2070

Alfa AF: 0.656 Hom.: 52202

Bravo AF: 0.617

Asia WGS AF: 0.522 AC: 1817 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	0.24
DANN	Benign	0.40
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs11249608; hg19: chr5-178426319; COSMIC: COSV51437372;