rs17042407

Variant names:

• chr2-112801337-T-C
• rs17042407
• ENST00000762706.1:n.404+30441T>C

Variant summary

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

The ENST00000762706.1(ENSG00000299339):​n.404+30441T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,222 control chromosomes in the GnomAD database, including 4,038 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 0.23 (4038 hom., cov: 32)
• Consequence: ENSG00000299339 ENST00000762706.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.151
• Publications: 12 publications found

Genes affected

ENSG00000299339 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.258 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
ENSG00000299339	ENST00000762706.1	n.404+30441T>C		intron_variant	Intron 2 of 3
ENSG00000299339	ENST00000762707.1	n.499+30441T>C		intron_variant	Intron 2 of 2
ENSG00000299339	ENST00000762708.1	n.265+30441T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34431 AN: 152104 Hom.: 4038 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.226 AC: 34436 AN: 152222 Hom.: 4038 Cov.: 32 AF XY: 0.222 AC XY: 16512 AN XY: 74442

African (AFR) AF: 0.190 AC: 7898 AN: 41536

American (AMR) AF: 0.199 AC: 3043 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 931 AN: 3472

East Asian (EAS) AF: 0.199 AC: 1034 AN: 5184

South Asian (SAS) AF: 0.234 AC: 1127 AN: 4816

European-Finnish (FIN) AF: 0.175 AC: 1860 AN: 10610

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17730 AN: 67992

Other (OTH) AF: 0.227 AC: 479 AN: 2110

Alfa AF: 0.249 Hom.: 19995

Bravo AF: 0.225

Asia WGS AF: 0.216 AC: 750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.3
DANN	Benign	0.38
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs17042407; hg19: chr2-113558914;