rs4757122

Variant names:

• chr11-13187713-G-T
• rs4757122
• ENST00000741297.1:n.95-6202C>A

Variant summary

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

The ENST00000741297.1(ENSG00000296717):​n.95-6202C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.541 in 151,876 control chromosomes in the GnomAD database, including 23,311 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 0.54 (23311 hom., cov: 32)
• Consequence: ENSG00000296717 ENST00000741297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 3 publications found

Genes affected

ENSG00000296717 (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 = 0.639 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000741297.1. 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
	ENSG00000296717	ENST00000741297.1		n.95-6202C>A		intron	N/A
	ENSG00000296717	ENST00000741299.1		n.80-6202C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.541 AC: 82079 AN: 151756 Hom.: 23316 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.558

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.541 AC: 82097 AN: 151876 Hom.: 23311 Cov.: 32 AF XY: 0.532 AC XY: 39461 AN XY: 74210

African (AFR) AF: 0.385 AC: 15939 AN: 41424

American (AMR) AF: 0.586 AC: 8937 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.649 AC: 2247 AN: 3464

East Asian (EAS) AF: 0.351 AC: 1815 AN: 5170

South Asian (SAS) AF: 0.427 AC: 2057 AN: 4816

European-Finnish (FIN) AF: 0.505 AC: 5311 AN: 10510

Middle Eastern (MID) AF: 0.555 AC: 161 AN: 290

European-Non Finnish (NFE) AF: 0.644 AC: 43729 AN: 67926

Other (OTH) AF: 0.560 AC: 1182 AN: 2112

Alfa AF: 0.606 Hom.: 71871

Bravo AF: 0.542

Asia WGS AF: 0.396 AC: 1378 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.1
DANN	Benign	0.46
PhyloP100		0.17

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: rs4757122;

hg19: chr11-13209260;