rs10240556

Positions:

• chr7-13291118-C-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000639998.1(ENSG00000229618):​n.608-19091C>G 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 0.0365 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: ENST00000639998.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.694

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000639998.1	n.608-19091C>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0478

Gnomad4 AMR AF: 0.0302

Gnomad4 ASJ AF: 0.0230

Gnomad4 EAS AF: 0.203

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.00679

Gnomad4 NFE AF: 0.0183

Gnomad4 OTH AF: 0.0398

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10240556; hg19: chr7-13330743;