rs3850493

Variant names:

• chr7-158961557-T-C
• rs3850493
• ENST00000752450.1:n.689+2646T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000752450.1(ENSG00000298006):​n.689+2646T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0699 in 152,190 control chromosomes in the GnomAD database, including 1,076 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 0.070 (1076 hom., cov: 33)
• Consequence: ENSG00000298006 ENST00000752450.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.400
• Publications: 3 publications found

Genes affected

ENSG00000298006 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.484 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
ENSG00000298006	ENST00000752450.1	n.689+2646T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0699 AC: 10635 AN: 152072 Hom.: 1080 Cov.: 33

Gnomad AFR AF: 0.0534

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.0752

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.0262

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0288

Gnomad OTH AF: 0.0817

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

GnomAD4 genome AF: 0.0699 AC: 10645 AN: 152190 Hom.: 1076 Cov.: 33 AF XY: 0.0774 AC XY: 5756 AN XY: 74406

African (AFR) AF: 0.0536 AC: 2225 AN: 41534

American (AMR) AF: 0.139 AC: 2121 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0752 AC: 261 AN: 3472

East Asian (EAS) AF: 0.500 AC: 2571 AN: 5146

South Asian (SAS) AF: 0.213 AC: 1025 AN: 4808

European-Finnish (FIN) AF: 0.0262 AC: 278 AN: 10608

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0288 AC: 1956 AN: 68012

Other (OTH) AF: 0.0833 AC: 176 AN: 2114

Alfa AF: 0.0494 Hom.: 943

Bravo AF: 0.0772

Asia WGS AF: 0.307 AC: 1066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.7
DANN	Benign	0.68
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs3850493; hg19: chr7-158754248;