rs10953515

chr7-106653236-G-A

Variant summary

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

The ENST00000490856.5(ENSG00000243797):n.109-42773C>T 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 0.251 in 152,088 control chromosomes in the GnomAD database, including 5,447 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 0.25 (5447 hom., cov: 32)
• Consequence: ENST00000490856.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.362 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.109-42773C>T		intron_variant, non_coding_transcript_variant		4
	ENST00000592441.1	n.173-42773C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38148 AN: 151970 Hom.: 5443 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.251 AC: 38172 AN: 152088 Hom.: 5447 Cov.: 32 AF XY: 0.254 AC XY: 18855 AN XY: 74350

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.261

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.265

Alfa AF: 0.287 Hom.: 2919

Bravo AF: 0.252

Asia WGS AF: 0.241 AC: 835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.8
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10953515; hg19: chr7-106293682;