rs1024034

Variant names:

• chr4-11435538-A-G
• rs1024034
• ENST00000656610.1:n.3723+1123A>G

Variant summary

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

The ENST00000656610.1(ENSG00000287778):​n.3723+1123A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0758 in 152,262 control chromosomes in the GnomAD database, including 904 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 0.076 (904 hom., cov: 32)
• Consequence: ENSG00000287778 ENST00000656610.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.450
• Publications: 2 publications found

Genes affected

ENSG00000287778 (HGNC:58736):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656610.1. 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
	ENSG00000287778	ENST00000656610.1		n.3723+1123A>G		intron	N/A
	ENSG00000287778	ENST00000662830.1		n.312+1123A>G		intron	N/A
	ENSG00000287778	ENST00000670155.1		n.431+1123A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0757 AC: 11516 AN: 152144 Hom.: 900 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0488

Gnomad ASJ AF: 0.0774

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0325

Gnomad FIN AF: 0.0138

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0294

Gnomad OTH AF: 0.0707

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

GnomAD4 genome AF: 0.0758 AC: 11535 AN: 152262 Hom.: 904 Cov.: 32 AF XY: 0.0737 AC XY: 5486 AN XY: 74440

African (AFR) AF: 0.194 AC: 8040 AN: 41516

American (AMR) AF: 0.0487 AC: 745 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0774 AC: 268 AN: 3464

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.0323 AC: 156 AN: 4830

European-Finnish (FIN) AF: 0.0138 AC: 147 AN: 10628

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0294 AC: 2003 AN: 68026

Other (OTH) AF: 0.0700 AC: 148 AN: 2114

Alfa AF: 0.0505 Hom.: 211

Bravo AF: 0.0829

Asia WGS AF: 0.0200 AC: 70 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.5
DANN	Benign	0.72
PhyloP100		0.45

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: rs1024034;

hg19: chr4-11437162;