chr5-1446604-C-G

Variant names:

• chr5-1446604-C-G
• rs2617596

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 0.46 in 151,534 control chromosomes in the GnomAD database, including 18,154 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 0.46 (18154 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.591 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: 0.461 AC: 69741 AN: 151424 Hom.: 18143 Cov.: 29

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.460 AC: 69775 AN: 151534 Hom.: 18154 Cov.: 29 AF XY: 0.458 AC XY: 33942 AN XY: 74054

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.468

Gnomad4 ASJ AF: 0.600

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.548

Gnomad4 NFE AF: 0.596

Gnomad4 OTH AF: 0.493

Alfa AF: 0.332 Hom.: 759

Bravo AF: 0.440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2617596; hg19: chr5-1446719; COSMIC: COSV54362736;