chr7-41261234-G-A

Variant names:

• chr7-41261234-G-A
• rs11505535
• ENST00000790257.1:n.312-11153G>A

Variant summary

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

The ENST00000790257.1(ENSG00000302889):​n.312-11153G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 151,900 control chromosomes in the GnomAD database, including 13,490 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 0.41 (13490 hom., cov: 32)
• Consequence: ENSG00000302889 ENST00000790257.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.445
• Publications: 0 publications found

Genes affected

ENSG00000302889 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.492 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
ENSG00000302889	ENST00000790257.1	n.312-11153G>A		intron_variant	Intron 2 of 7

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62408 AN: 151780 Hom.: 13472 Cov.: 32

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.411 AC: 62470 AN: 151900 Hom.: 13490 Cov.: 32 AF XY: 0.403 AC XY: 29901 AN XY: 74216

African (AFR) AF: 0.497 AC: 20592 AN: 41398

American (AMR) AF: 0.351 AC: 5354 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1509 AN: 3470

East Asian (EAS) AF: 0.182 AC: 935 AN: 5150

South Asian (SAS) AF: 0.258 AC: 1238 AN: 4806

European-Finnish (FIN) AF: 0.293 AC: 3093 AN: 10540

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28187 AN: 67960

Other (OTH) AF: 0.424 AC: 898 AN: 2116

Alfa AF: 0.383 Hom.: 6168

Bravo AF: 0.422

Asia WGS AF: 0.216 AC: 754 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	2.1
DANN	Benign	0.66
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs11505535; hg19: chr7-41300832;