5-149646318-G-A

Position:

• chr5-149646318-G-A

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 0.573 in 151,822 control chromosomes in the GnomAD database, including 25,536 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 0.57 (25536 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.661 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: 0.573 AC: 86971 AN: 151704 Hom.: 25530 Cov.: 30

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.573 AC: 87020 AN: 151822 Hom.: 25536 Cov.: 30 AF XY: 0.575 AC XY: 42665 AN XY: 74156

Gnomad4 AFR AF: 0.448

Gnomad4 AMR AF: 0.496

Gnomad4 ASJ AF: 0.680

Gnomad4 EAS AF: 0.680

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.691

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.614

Alfa AF: 0.595 Hom.: 7100

Bravo AF: 0.551

Asia WGS AF: 0.588 AC: 2046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.93
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10065816; hg19: chr5-149025881;