rs7250738

Variant names:

• chr19-7735336-C-T
• rs7250738
• ENST00000678003.1:n.*291-1362G>A

Variant summary

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

The ENST00000678003.1(ENSG00000288669):​n.*291-1362G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.938 in 152,260 control chromosomes in the GnomAD database, including 67,212 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 0.94 (67212 hom., cov: 31)
• Consequence: ENSG00000288669 ENST00000678003.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.361

Genes affected

ENSG00000288669 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.967 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
ENSG00000288669	ENST00000678003.1	n.*291-1362G>A		intron_variant	Intron 2 of 12			ENSP00000504497.1
ENSG00000288669	ENST00000676543.1	n.71-1362G>A		intron_variant	Intron 1 of 11			ENSP00000503143.1
ENSG00000288669	ENST00000678227.1	n.580-1380G>A		intron_variant	Intron 1 of 1
ENSG00000288669	ENST00000678780.1	n.*1795-1362G>A		intron_variant	Intron 4 of 12			ENSP00000503751.1

Frequencies

GnomAD3 genomes AF: 0.938 AC: 142661 AN: 152142 Hom.: 67153 Cov.: 31

Gnomad AFR AF: 0.897

Gnomad AMI AF: 0.975

Gnomad AMR AF: 0.938

Gnomad ASJ AF: 0.972

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.875

Gnomad FIN AF: 0.987

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.974

Gnomad OTH AF: 0.952

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

GnomAD4 genome AF: 0.938 AC: 142780 AN: 152260 Hom.: 67212 Cov.: 31 AF XY: 0.934 AC XY: 69543 AN XY: 74442

Gnomad4 AFR AF: 0.898

Gnomad4 AMR AF: 0.938

Gnomad4 ASJ AF: 0.972

Gnomad4 EAS AF: 0.708

Gnomad4 SAS AF: 0.875

Gnomad4 FIN AF: 0.987

Gnomad4 NFE AF: 0.974

Gnomad4 OTH AF: 0.952

Alfa AF: 0.955 Hom.: 12085

Bravo AF: 0.933

Asia WGS AF: 0.816 AC: 2838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7250738; hg19: chr19-7800222;