rs752237

Variant names:

• chr19-33240894-G-A
• rs752237
• ENST00000762495.1:n.165-1049C>T

Variant summary

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

The ENST00000762495.1(ENSG00000299313):​n.165-1049C>T 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 152,158 control chromosomes in the GnomAD database, including 3,596 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 (3596 hom., cov: 34)
• Consequence: ENSG00000299313 ENST00000762495.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0930
• Publications: 5 publications found

Genes affected

ENSG00000299313 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.336 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
ENSG00000299313	ENST00000762495.1	n.165-1049C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29872 AN: 152040 Hom.: 3594 Cov.: 34

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.196 AC: 29881 AN: 152158 Hom.: 3596 Cov.: 34 AF XY: 0.198 AC XY: 14751 AN XY: 74370

African (AFR) AF: 0.340 AC: 14119 AN: 41502

American (AMR) AF: 0.153 AC: 2341 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 548 AN: 3470

East Asian (EAS) AF: 0.299 AC: 1540 AN: 5154

South Asian (SAS) AF: 0.193 AC: 929 AN: 4820

European-Finnish (FIN) AF: 0.144 AC: 1527 AN: 10598

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8357 AN: 67998

Other (OTH) AF: 0.163 AC: 345 AN: 2114

Alfa AF: 0.146 Hom.: 941

Bravo AF: 0.204

Asia WGS AF: 0.199 AC: 693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.3
DANN	Benign	0.58
PhyloP100		0.093

Splicing

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

Other links and lift over

dbSNP: rs752237; hg19: chr19-33731800;