rs2903698

Positions:

• 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, non coding transcript 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: ENST00000507739.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.998

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000507739.5	n.98+6473A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000510744.1	n.332+26353T>C		intron_variant, non_coding_transcript_variant		3
	ENST00000515230.1	n.76-130A>G		intron_variant, non_coding_transcript_variant		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;