chr4-11119136-T-C

Variant names:

• chr4-11119136-T-C
• rs7662694
• ENST00000754158.1:n.196-1628T>C

Variant summary

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

The ENST00000754158.1(ENSG00000298262):​n.196-1628T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 152,012 control chromosomes in the GnomAD database, including 5,168 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 0.25 (5168 hom., cov: 32)
• Consequence: ENSG00000298262 ENST00000754158.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.311
• Publications: 0 publications found

Genes affected

ENSG00000298262 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000754158.1. 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
	ENSG00000298262	ENST00000754158.1		n.196-1628T>C		intron	N/A
	ENSG00000298262	ENST00000754159.1		n.495-1628T>C		intron	N/A
	ENSG00000298262	ENST00000754160.1		n.487-42627T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38538 AN: 151894 Hom.: 5160 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.254 AC: 38574 AN: 152012 Hom.: 5168 Cov.: 32 AF XY: 0.260 AC XY: 19313 AN XY: 74302

African (AFR) AF: 0.223 AC: 9240 AN: 41476

American (AMR) AF: 0.356 AC: 5429 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1002 AN: 3470

East Asian (EAS) AF: 0.435 AC: 2250 AN: 5170

South Asian (SAS) AF: 0.231 AC: 1116 AN: 4824

European-Finnish (FIN) AF: 0.303 AC: 3194 AN: 10526

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15265 AN: 67970

Other (OTH) AF: 0.250 AC: 528 AN: 2110

Alfa AF: 0.237 Hom.: 941

Bravo AF: 0.262

Asia WGS AF: 0.336 AC: 1164 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.1
DANN	Benign	0.80
PhyloP100		0.31

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: rs7662694;

hg19: chr4-11120760;