rs2865703

Positions:

• chr4-95726437-T-C
• chr4-95726437-T-G

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 0.728 in 152,160 control chromosomes in the GnomAD database, including 42,576 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 0.73 (42576 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.37

Genes affected

(HGNC:):

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 = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.95726437T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.728 AC: 110704 AN: 152042 Hom.: 42557 Cov.: 33

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.907

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.863

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.877

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.728 AC: 110761 AN: 152160 Hom.: 42576 Cov.: 33 AF XY: 0.722 AC XY: 53724 AN XY: 74372

Gnomad4 AFR AF: 0.491

Gnomad4 AMR AF: 0.670

Gnomad4 ASJ AF: 0.719

Gnomad4 EAS AF: 0.627

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.863

Gnomad4 NFE AF: 0.877

Gnomad4 OTH AF: 0.738

Alfa AF: 0.817 Hom.: 25400

Bravo AF: 0.707

Asia WGS AF: 0.580 AC: 2022 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	0.14
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2865703; hg19: chr4-96647588;