5-149644765-T-C

Position:

• chr5-149644765-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.609

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.692

Gnomad4 NFE AF: 0.662

Gnomad4 OTH AF: 0.639

Alfa AF: 0.639 Hom.: 42533

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4705360; hg19: chr5-149024328;