chr5-149644765-T-C

Variant names:

• chr5-149644765-T-C
• rs4705360

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 152,048 control chromosomes in the GnomAD database, including 29,057 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 (29057 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.657 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: 0.611 AC: 92892 AN: 151930 Hom.: 29032 Cov.: 32

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.641

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

GnomAD4 genome AF: 0.611 AC: 92969 AN: 152048 Hom.: 29057 Cov.: 32 AF XY: 0.605 AC XY: 44978 AN XY: 74338

African (AFR) AF: 0.609 AC: 25242 AN: 41456

American (AMR) AF: 0.498 AC: 7606 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2290 AN: 3470

East Asian (EAS) AF: 0.272 AC: 1404 AN: 5168

South Asian (SAS) AF: 0.424 AC: 2043 AN: 4824

European-Finnish (FIN) AF: 0.692 AC: 7329 AN: 10592

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.662 AC: 44968 AN: 67948

Other (OTH) AF: 0.639 AC: 1350 AN: 2114

Alfa AF: 0.640 Hom.: 50504

Bravo AF: 0.596

Asia WGS AF: 0.387 AC: 1348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.4
DANN	Benign	0.54
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs4705360; hg19: chr5-149024328;