rs342240

Variant names:

• chr7-106696804-G-A
• rs342240
• ENST00000490856.5:n.108+35538C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-106696804-G-A
• chr7-106696804-G-C

Variant summary

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

The ENST00000592441.1(ENSG00000243797):​n.172+63762C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 151,990 control chromosomes in the GnomAD database, including 9,892 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 0.35 (9892 hom., cov: 32)
• Consequence: ENSG00000243797 ENST00000592441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.647

Genes affected

ENSG00000243797 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.424 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+35538C>T		intron_variant	Intron 1 of 4	4
ENSG00000243797	ENST00000592441.1	n.172+63762C>T		intron_variant	Intron 2 of 4	2

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52856 AN: 151872 Hom.: 9893 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.348 AC: 52865 AN: 151990 Hom.: 9892 Cov.: 32 AF XY: 0.348 AC XY: 25836 AN XY: 74278

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.428

Gnomad4 OTH AF: 0.333

Alfa AF: 0.401 Hom.: 25065

Bravo AF: 0.331

Asia WGS AF: 0.290 AC: 1013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.95
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs342240; hg19: chr7-106337250;