10-100342375-G-C

Position:

• chr10-100342375-G-C

Variant summary

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

The variant allele was found at a frequency of 0.45 in 151,974 control chromosomes in the GnomAD database, including 16,109 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 0.45 (16109 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.100342375G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000231188	ENST00000429420.1	n.211+350C>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68302 AN: 151856 Hom.: 16095 Cov.: 32

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.450 AC: 68362 AN: 151974 Hom.: 16109 Cov.: 32 AF XY: 0.454 AC XY: 33737 AN XY: 74288

Gnomad4 AFR AF: 0.599

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.465

Gnomad4 FIN AF: 0.458

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.434

Alfa AF: 0.284 Hom.: 747

Bravo AF: 0.445

Asia WGS AF: 0.437 AC: 1520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.61
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: rs11190478; hg19: chr10-102102132;