5-75274031-G-T

Variant names:

• chr5-75274031-G-T
• rs4704200

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 0.515 in 152,010 control chromosomes in the GnomAD database, including 21,209 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 0.52 (21209 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.686 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: 0.515 AC: 78204 AN: 151892 Hom.: 21171 Cov.: 32

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.515 AC: 78305 AN: 152010 Hom.: 21209 Cov.: 32 AF XY: 0.518 AC XY: 38507 AN XY: 74290

African (AFR) AF: 0.693 AC: 28742 AN: 41466

American (AMR) AF: 0.473 AC: 7232 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1789 AN: 3470

East Asian (EAS) AF: 0.556 AC: 2866 AN: 5158

South Asian (SAS) AF: 0.598 AC: 2879 AN: 4816

European-Finnish (FIN) AF: 0.451 AC: 4756 AN: 10544

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28479 AN: 67956

Other (OTH) AF: 0.508 AC: 1072 AN: 2112

Alfa AF: 0.461 Hom.: 23743

Bravo AF: 0.521

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.40
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs4704200; hg19: chr5-74569856;