rs4014195

Variant names:

• chr11-65739351-C-G
• rs4014195
• ENST00000744235.1:n.284+4493G>C

Your query was ambiguous. Multiple possible variants found:

• chr11-65739351-C-G
• chr11-65739351-C-T

Variant summary

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

The ENST00000744235.1(ENSG00000297007):​n.284+4493G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 151,890 control chromosomes in the GnomAD database, including 7,927 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 0.31 (7927 hom., cov: 30)
• Consequence: ENSG00000297007 ENST00000744235.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• Publications: 47 publications found

Genes affected

ENSG00000297007 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297007	ENST00000744235.1	n.284+4493G>C		intron_variant	Intron 1 of 3
ENSG00000297007	ENST00000744236.1	n.249+4493G>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47067 AN: 151772 Hom.: 7923 Cov.: 30

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.310 AC: 47095 AN: 151890 Hom.: 7927 Cov.: 30 AF XY: 0.317 AC XY: 23537 AN XY: 74216

African (AFR) AF: 0.211 AC: 8759 AN: 41428

American (AMR) AF: 0.250 AC: 3811 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1392 AN: 3470

East Asian (EAS) AF: 0.227 AC: 1173 AN: 5164

South Asian (SAS) AF: 0.367 AC: 1769 AN: 4818

European-Finnish (FIN) AF: 0.482 AC: 5066 AN: 10518

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.355 AC: 24144 AN: 67922

Other (OTH) AF: 0.314 AC: 664 AN: 2114

Alfa AF: 0.345 Hom.: 5081

Bravo AF: 0.283

Asia WGS AF: 0.263 AC: 915 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.0
DANN	Benign	0.81
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs4014195; hg19: chr11-65506822;