5-1299098-A-G

Variant names:

• chr5-1299098-A-G
• rs2735948

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 0.644 in 151,964 control chromosomes in the GnomAD database, including 32,047 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 0.64 (32047 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.811 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: 0.644 AC: 97812 AN: 151846 Hom.: 32000 Cov.: 32

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.644 AC: 97918 AN: 151964 Hom.: 32047 Cov.: 32 AF XY: 0.650 AC XY: 48246 AN XY: 74252

African (AFR) AF: 0.709 AC: 29381 AN: 41446

American (AMR) AF: 0.680 AC: 10379 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 2002 AN: 3468

East Asian (EAS) AF: 0.801 AC: 4128 AN: 5154

South Asian (SAS) AF: 0.832 AC: 4008 AN: 4816

European-Finnish (FIN) AF: 0.594 AC: 6259 AN: 10544

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.587 AC: 39896 AN: 67950

Other (OTH) AF: 0.612 AC: 1293 AN: 2112

Alfa AF: 0.603 Hom.: 19087

Bravo AF: 0.650

Asia WGS AF: 0.823 AC: 2859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.8
DANN	Benign	0.71
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs2735948; hg19: chr5-1299213;