rs10488418

Variant names:

• chr7-136421818-G-A
• rs10488418
• ENST00000435996.1:n.359-15234G>A

Variant summary

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

The ENST00000435996.1(ENSG00000232053):​n.359-15234G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0396 in 152,112 control chromosomes in the GnomAD database, including 294 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 0.040 (294 hom., cov: 32)
• Consequence: ENSG00000232053 ENST00000435996.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161
• Publications: 1 publications found

Genes affected

ENSG00000232053 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375523	NR_187956.1	n.438-15234G>A		intron_variant	Intron 4 of 4
LOC105375523	NR_187957.1	n.731-15234G>A		intron_variant	Intron 5 of 5
LOC105375523	NR_187960.1	n.778-15234G>A		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000232053	ENST00000435996.1	n.359-15234G>A		intron_variant	Intron 3 of 3	3
ENSG00000232053	ENST00000437569.1	n.55-15234G>A		intron_variant	Intron 1 of 1	3
ENSG00000232053	ENST00000445293.6	n.778-15234G>A		intron_variant	Intron 6 of 6	5

Frequencies

GnomAD3 genomes AF: 0.0394 AC: 5995 AN: 151996 Hom.: 291 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0197

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.0216

Gnomad SAS AF: 0.0271

Gnomad FIN AF: 0.00841

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00775

Gnomad OTH AF: 0.0326

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

GnomAD4 genome AF: 0.0396 AC: 6017 AN: 152112 Hom.: 294 Cov.: 32 AF XY: 0.0391 AC XY: 2906 AN XY: 74372

African (AFR) AF: 0.114 AC: 4742 AN: 41484

American (AMR) AF: 0.0196 AC: 300 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.00317 AC: 11 AN: 3472

East Asian (EAS) AF: 0.0214 AC: 111 AN: 5184

South Asian (SAS) AF: 0.0271 AC: 131 AN: 4828

European-Finnish (FIN) AF: 0.00841 AC: 89 AN: 10584

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.00775 AC: 527 AN: 67970

Other (OTH) AF: 0.0327 AC: 69 AN: 2108

Alfa AF: 0.0286 Hom.: 17

Bravo AF: 0.0428

Asia WGS AF: 0.0380 AC: 133 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.94
PhyloP100		-0.16
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10488418; hg19: chr7-136106566;