rs2472649

Positions:

• chr4-73991991-A-G
• chr4-73991991-A-T

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 0.644 in 152,142 control chromosomes in the GnomAD database, including 37,594 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 (37594 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.73991991A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.645 AC: 98054 AN: 152024 Hom.: 37600 Cov.: 33

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.831

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.644 AC: 98045 AN: 152142 Hom.: 37594 Cov.: 33 AF XY: 0.650 AC XY: 48325 AN XY: 74370

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.733

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.832

Gnomad4 SAS AF: 0.753

Gnomad4 FIN AF: 0.849

Gnomad4 NFE AF: 0.831

Gnomad4 OTH AF: 0.673

Alfa AF: 0.802 Hom.: 73592

Bravo AF: 0.612

Asia WGS AF: 0.694 AC: 2409 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2472649; hg19: chr4-74857708;