rs7735699

Variant names:

• chr5-79803641-A-C
• rs7735699
• ENST00000421252.2:n.125+197T>G

Variant summary

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

The ENST00000421252.2(ENSG00000250258):​n.125+197T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 152,118 control chromosomes in the GnomAD database, including 6,885 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 0.27 (6885 hom., cov: 31)
• Consequence: ENSG00000250258 ENST00000421252.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230

Genes affected

ENSG00000250258 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.377 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
ENSG00000250258	ENST00000421252.2	n.125+197T>G		intron_variant	Intron 2 of 4	3

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41564 AN: 152000 Hom.: 6884 Cov.: 31

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.273 AC: 41553 AN: 152118 Hom.: 6885 Cov.: 31 AF XY: 0.269 AC XY: 20015 AN XY: 74356

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.340

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.278

Alfa AF: 0.319 Hom.: 2467

Bravo AF: 0.258

Asia WGS AF: 0.165 AC: 572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7735699; hg19: chr5-79099464;