10-49227831-T-C

Position:

• chr10-49227831-T-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 0.954 in 152,310 control chromosomes in the GnomAD database, including 69,615 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 0.95 (69615 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.642

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.987 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.49227831T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.954 AC: 145228 AN: 152192 Hom.: 69585 Cov.: 33

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.975

Gnomad AMR AF: 0.981

Gnomad ASJ AF: 0.982

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.987

Gnomad FIN AF: 0.996

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.994

Gnomad OTH AF: 0.970

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

GnomAD4 genome AF: 0.954 AC: 145315 AN: 152310 Hom.: 69615 Cov.: 33 AF XY: 0.956 AC XY: 71193 AN XY: 74484

Gnomad4 AFR AF: 0.856

Gnomad4 AMR AF: 0.981

Gnomad4 ASJ AF: 0.982

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.987

Gnomad4 FIN AF: 0.996

Gnomad4 NFE AF: 0.994

Gnomad4 OTH AF: 0.970

Alfa AF: 0.978 Hom.: 14773

Bravo AF: 0.947

Asia WGS AF: 0.967 AC: 3361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.3
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7912808; hg19: chr10-50435876;