rs11942914

Variant names:

• chr4-129367465-A-G
• rs11942914
• ENST00000659495.1:n.112-4280T>C

Variant summary

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

The ENST00000659495.1(ENSG00000287748):​n.112-4280T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0914 in 152,250 control chromosomes in the GnomAD database, including 864 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 0.091 (864 hom., cov: 33)
• Consequence: ENSG00000287748 ENST00000659495.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.49
• Publications: 0 publications found

Genes affected

ENSG00000287748 (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 = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377417	XR_939191.3	n.365-4280T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287748	ENST00000659495.1	n.112-4280T>C		intron_variant	Intron 1 of 1
ENSG00000287748	ENST00000723085.1	n.276-4280T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0914 AC: 13899 AN: 152132 Hom.: 862 Cov.: 33

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.0579

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.0601

Gnomad FIN AF: 0.0554

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0512

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.0914 AC: 13921 AN: 152250 Hom.: 864 Cov.: 33 AF XY: 0.0929 AC XY: 6914 AN XY: 74438

African (AFR) AF: 0.137 AC: 5671 AN: 41540

American (AMR) AF: 0.167 AC: 2550 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0579 AC: 201 AN: 3470

East Asian (EAS) AF: 0.169 AC: 874 AN: 5184

South Asian (SAS) AF: 0.0595 AC: 287 AN: 4820

European-Finnish (FIN) AF: 0.0554 AC: 587 AN: 10600

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0512 AC: 3480 AN: 68022

Other (OTH) AF: 0.100 AC: 212 AN: 2112

Alfa AF: 0.0619 Hom.: 176

Bravo AF: 0.105

Asia WGS AF: 0.122 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.0
DANN	Benign	0.81
PhyloP100		2.5

Splicing

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

Other links and lift over

dbSNP: rs11942914; hg19: chr4-130288620;