rs342247

chr7-106702745-A-Gchr7-106702745-A-T

Variant summary

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

The ENST00000490856.5(ENSG00000243797):n.108+29597T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 151,232 control chromosomes in the GnomAD database, including 9,867 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 (9867 hom., cov: 31)
• Consequence: ENST00000490856.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.474

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000490856.5	n.108+29597T>C		intron_variant, non_coding_transcript_variant		4
	ENST00000592441.1	n.172+57821T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52452 AN: 151116 Hom.: 9869 Cov.: 31

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.347 AC: 52462 AN: 151232 Hom.: 9867 Cov.: 31 AF XY: 0.347 AC XY: 25627 AN XY: 73884

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.445

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.337

Alfa AF: 0.388 Hom.: 2085

Bravo AF: 0.329

Asia WGS AF: 0.290 AC: 1005 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.9
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs342247; hg19: chr7-106343191;