rs7735699

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

Genes affected

ENSG00000250258 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000421252.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000250258	ENST00000421252.2	TSL:3	n.125+197T>G		intron	N/A
	ENSG00000286818	ENST00000827626.1		n.83+1887A>C		intron	N/A

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

African (AFR) AF: 0.103 AC: 4266 AN: 41536

American (AMR) AF: 0.260 AC: 3973 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1182 AN: 3472

East Asian (EAS) AF: 0.101 AC: 525 AN: 5180

South Asian (SAS) AF: 0.286 AC: 1375 AN: 4814

European-Finnish (FIN) AF: 0.317 AC: 3354 AN: 10566

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25862 AN: 67968

Other (OTH) AF: 0.278 AC: 588 AN: 2114

Alfa AF: 0.329 Hom.: 17444

Bravo AF: 0.258

Asia WGS AF: 0.165 AC: 572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.75
PhyloP100		-0.023

Splicing

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

Other links and lift over

dbSNP: rs7735699; hg19: chr5-79099464;