rs10953515

Variant names:

• chr7-106653236-G-A
• rs10953515
• ENST00000490856.5:n.109-42773C>T

Variant summary

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

The ENST00000592441.1(ENSG00000243797):​n.173-42773C>T variant causes a intron 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: ENSG00000243797 ENST00000592441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• Publications: 5 publications found

Genes affected

ENSG00000243797 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000592441.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000243797	ENST00000490856.5	TSL:4	n.109-42773C>T		intron	N/A
	ENSG00000243797	ENST00000592441.1	TSL:2	n.173-42773C>T		intron	N/A

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

African (AFR) AF: 0.109 AC: 4521 AN: 41494

American (AMR) AF: 0.370 AC: 5652 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1034 AN: 3468

East Asian (EAS) AF: 0.244 AC: 1259 AN: 5168

South Asian (SAS) AF: 0.261 AC: 1263 AN: 4830

European-Finnish (FIN) AF: 0.285 AC: 3021 AN: 10588

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20517 AN: 67960

Other (OTH) AF: 0.265 AC: 559 AN: 2106

Alfa AF: 0.283 Hom.: 4403

Bravo AF: 0.252

Asia WGS AF: 0.241 AC: 835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.32
PhyloP100		-0.011

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10953515;

hg19: chr7-106293682;