rs342275

Variant names:

• chr7-106718770-C-T
• rs342275
• ENST00000490856.5:n.108+13572G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000592441.1(ENSG00000243797):​n.172+41796G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 151,966 control chromosomes in the GnomAD database, including 9,726 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 0.33 (9726 hom., cov: 32)
• Consequence: ENSG00000243797 ENST00000592441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830

Genes affected

ENSG00000243797 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.432 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
ENSG00000243797	ENST00000490856.5	n.108+13572G>A		intron_variant	Intron 1 of 4	4
ENSG00000243797	ENST00000592441.1	n.172+41796G>A		intron_variant	Intron 2 of 4	2

Frequencies

GnomAD3 genomes AF: 0.329 AC: 49936 AN: 151848 Hom.: 9726 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.329 AC: 49935 AN: 151966 Hom.: 9726 Cov.: 32 AF XY: 0.330 AC XY: 24516 AN XY: 74254

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.237

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.458

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.329

Alfa AF: 0.353 Hom.: 986

Bravo AF: 0.307

Asia WGS AF: 0.301 AC: 1050 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs342275; hg19: chr7-106359216;