chr11-75703241-G-A

Variant names:

• chr11-75703241-G-A
• rs7120248
• ENST00000770408.1:n.182-302C>T

Variant summary

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

The ENST00000770408.1(ENSG00000300258):​n.182-302C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 152,130 control chromosomes in the GnomAD database, including 6,258 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 (6258 hom., cov: 32)
• Consequence: ENSG00000300258 ENST00000770408.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.316
• Publications: 4 publications found

Genes affected

ENSG00000300258 (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 = 0.359 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369392	XR_950316.4	n.81-302C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300258	ENST00000770408.1	n.182-302C>T		intron_variant	Intron 1 of 2
ENSG00000300258	ENST00000770409.1	n.164-302C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41199 AN: 152012 Hom.: 6254 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.0719

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.271 AC: 41213 AN: 152130 Hom.: 6258 Cov.: 32 AF XY: 0.263 AC XY: 19529 AN XY: 74354

African (AFR) AF: 0.162 AC: 6712 AN: 41504

American (AMR) AF: 0.249 AC: 3815 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 984 AN: 3472

East Asian (EAS) AF: 0.0722 AC: 374 AN: 5178

South Asian (SAS) AF: 0.219 AC: 1056 AN: 4812

European-Finnish (FIN) AF: 0.251 AC: 2658 AN: 10572

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24685 AN: 67988

Other (OTH) AF: 0.294 AC: 620 AN: 2106

Alfa AF: 0.331 Hom.: 39052

Bravo AF: 0.266

Asia WGS AF: 0.152 AC: 529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.73
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs7120248; hg19: chr11-75414286;