chr11-120101740-A-T

Variant names:

• chr11-120101740-A-T
• rs1073636
• ENST00000747543.1:n.66+6555T>A

Variant summary

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

The ENST00000747543.1(ENSG00000297377):​n.66+6555T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 152,028 control chromosomes in the GnomAD database, including 18,107 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 0.48 (18107 hom., cov: 32)
• Consequence: ENSG00000297377 ENST00000747543.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 7 publications found

Genes affected

ENSG00000297377 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378956	XR_001748415.1	n.76+539T>A		intron_variant	Intron 1 of 2
LOC105378956	XR_001748416.1	n.76+539T>A		intron_variant	Intron 1 of 2
LOC105378956	XR_948099.2	n.76+539T>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297377	ENST00000747543.1	n.66+6555T>A		intron_variant	Intron 1 of 1
ENSG00000297377	ENST00000747544.1	n.73+539T>A		intron_variant	Intron 1 of 2
ENSG00000297377	ENST00000747545.1	n.73+539T>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72888 AN: 151908 Hom.: 18098 Cov.: 32

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.650

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.480 AC: 72927 AN: 152028 Hom.: 18107 Cov.: 32 AF XY: 0.473 AC XY: 35133 AN XY: 74276

African (AFR) AF: 0.454 AC: 18833 AN: 41442

American (AMR) AF: 0.401 AC: 6131 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1801 AN: 3468

East Asian (EAS) AF: 0.120 AC: 621 AN: 5168

South Asian (SAS) AF: 0.329 AC: 1585 AN: 4824

European-Finnish (FIN) AF: 0.525 AC: 5548 AN: 10562

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.539 AC: 36618 AN: 67952

Other (OTH) AF: 0.486 AC: 1028 AN: 2116

Alfa AF: 0.505 Hom.: 2467

Bravo AF: 0.469

Asia WGS AF: 0.236 AC: 821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.017
DANN	Benign	0.36
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1073636; hg19: chr11-119972448;