rs10240556

Variant names:

• chr7-13291118-C-G
• rs10240556
• ENST00000411542.1:n.237-19091C>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000411542.1(ENSG00000229618):​n.237-19091C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0365 in 152,218 control chromosomes in the GnomAD database, including 218 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 0.037 (218 hom., cov: 32)
• Consequence: ENSG00000229618 ENST00000411542.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.694
• Publications: 0 publications found

Genes affected

ENSG00000229618 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.193 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
ENSG00000229618	ENST00000411542.1	n.237-19091C>G		intron_variant	Intron 2 of 4	4
ENSG00000229618	ENST00000638964.1	n.609-19091C>G		intron_variant	Intron 2 of 5	5
ENSG00000229618	ENST00000639998.1	n.608-19091C>G		intron_variant	Intron 4 of 7	5

Frequencies

GnomAD3 genomes AF: 0.0365 AC: 5553 AN: 152100 Hom.: 218 Cov.: 32

Gnomad AFR AF: 0.0475

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0303

Gnomad ASJ AF: 0.0230

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.00679

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0183

Gnomad OTH AF: 0.0383

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

GnomAD4 genome AF: 0.0365 AC: 5558 AN: 152218 Hom.: 218 Cov.: 32 AF XY: 0.0378 AC XY: 2816 AN XY: 74406

African (AFR) AF: 0.0478 AC: 1986 AN: 41530

American (AMR) AF: 0.0302 AC: 462 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0230 AC: 80 AN: 3472

East Asian (EAS) AF: 0.203 AC: 1050 AN: 5180

South Asian (SAS) AF: 0.101 AC: 485 AN: 4820

European-Finnish (FIN) AF: 0.00679 AC: 72 AN: 10604

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0183 AC: 1242 AN: 68010

Other (OTH) AF: 0.0398 AC: 84 AN: 2112

Alfa AF: 0.0239 Hom.: 7

Bravo AF: 0.0387

Asia WGS AF: 0.148 AC: 515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	14
DANN	Benign	0.69
PhyloP100		0.69
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: rs10240556; hg19: chr7-13330743;