rs175990

Variant names:

• chr14-76942722-A-C
• rs175990
• ENST00000688632.2:n.120+5922T>G

Your query was ambiguous. Multiple possible variants found:

• chr14-76942722-A-C
• chr14-76942722-A-T

Variant summary

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

The ENST00000688632.2(ENSG00000288762):​n.120+5922T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 152,078 control chromosomes in the GnomAD database, including 4,095 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 0.22 (4095 hom., cov: 31)
• Consequence: ENSG00000288762 ENST00000688632.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24
• Publications: 2 publications found

Genes affected

ENSG00000288762 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.262 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
ENSG00000288762	ENST00000688632.2	n.120+5922T>G		intron_variant	Intron 1 of 4
ENSG00000288762	ENST00000692498.1	n.117+5922T>G		intron_variant	Intron 1 of 2
ENSG00000288762	ENST00000793557.1	n.101+5922T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34104 AN: 151960 Hom.: 4098 Cov.: 31

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.224 AC: 34098 AN: 152078 Hom.: 4095 Cov.: 31 AF XY: 0.223 AC XY: 16597 AN XY: 74362

African (AFR) AF: 0.151 AC: 6265 AN: 41480

American (AMR) AF: 0.244 AC: 3727 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 994 AN: 3468

East Asian (EAS) AF: 0.132 AC: 682 AN: 5172

South Asian (SAS) AF: 0.263 AC: 1266 AN: 4822

European-Finnish (FIN) AF: 0.211 AC: 2228 AN: 10582

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 18035 AN: 67968

Other (OTH) AF: 0.244 AC: 515 AN: 2110

Alfa AF: 0.266 Hom.: 9325

Bravo AF: 0.226

Asia WGS AF: 0.195 AC: 679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	9.5
DANN	Benign	0.84
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs175990; hg19: chr14-77409065;