5-4199643-C-T

Variant names:

• chr5-4199643-C-T
• rs10036180

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 0.929 in 152,264 control chromosomes in the GnomAD database, including 65,970 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 0.93 (65970 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.501
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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: 0.929 AC: 141419 AN: 152146 Hom.: 65943 Cov.: 33

Gnomad AFR AF: 0.855

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.957

Gnomad ASJ AF: 0.969

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.889

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.956

Gnomad OTH AF: 0.933

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

GnomAD4 genome AF: 0.929 AC: 141499 AN: 152264 Hom.: 65970 Cov.: 33 AF XY: 0.930 AC XY: 69234 AN XY: 74448

African (AFR) AF: 0.855 AC: 35500 AN: 41536

American (AMR) AF: 0.957 AC: 14639 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.969 AC: 3361 AN: 3470

East Asian (EAS) AF: 0.994 AC: 5127 AN: 5158

South Asian (SAS) AF: 0.889 AC: 4294 AN: 4832

European-Finnish (FIN) AF: 0.985 AC: 10459 AN: 10620

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.956 AC: 65013 AN: 68032

Other (OTH) AF: 0.924 AC: 1950 AN: 2110

Alfa AF: 0.945 Hom.: 20354

Bravo AF: 0.927

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.0
DANN	Benign	0.56
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs10036180; hg19: chr5-4199756;