rs1073636

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000747543.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297377	ENST00000747543.1		n.66+6555T>A		intron	N/A
	ENSG00000297377	ENST00000747544.1		n.73+539T>A		intron	N/A
	ENSG00000297377	ENST00000747545.1		n.73+539T>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1073636;

hg19: chr11-119972448;