rs2903698

Variant names:

• chr4-75407765-A-G
• rs2903698
• ENST00000507739.5:n.98+6473A>G

Your query was ambiguous. Multiple possible variants found:

• chr4-75407765-A-G
• chr4-75407765-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000507739.5(ENSG00000250735):​n.98+6473A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,200 control chromosomes in the GnomAD database, including 3,463 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 0.20 (3462 hom., cov: 32)
  • Exomes 𝑓: 0.28 (1 hom.)
• Consequence: ENSG00000250735 ENST00000507739.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.998

Genes affected

ENSG00000250735 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.251 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
ENSG00000250735	ENST00000507739.5	n.98+6473A>G		intron_variant	Intron 1 of 2	3
ENSG00000248646	ENST00000510744.1	n.332+26353T>C		intron_variant	Intron 1 of 1	3
ENSG00000250735	ENST00000515230.1	n.76-130A>G		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29795 AN: 152064 Hom.: 3456 Cov.: 32

Gnomad AFR AF: 0.0947

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.0943

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.175

GnomAD4 exome AF: 0.278 AC: 5 AN: 18 Hom.: 1 AF XY: 0.214 AC XY: 3 AN XY: 14

Gnomad4 NFE exome AF: 0.278

GnomAD4 genome AF: 0.196 AC: 29826 AN: 152182 Hom.: 3462 Cov.: 32 AF XY: 0.199 AC XY: 14799 AN XY: 74408

Gnomad4 AFR AF: 0.0952

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.0947

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.335

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.174

Alfa AF: 0.235 Hom.: 9323

Bravo AF: 0.179

Asia WGS AF: 0.147 AC: 514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.24
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2903698; hg19: chr4-76332975;