chr10-97349131-T-C

Position:

• chr10-97349131-T-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The variant allele was found at a frequency of 0.000684 in 147,680 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.00068 (0 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.000678 AC: 100 AN: 147556 Hom.: 0 Cov.: 28

Gnomad AFR AF: 0.0000493

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000746

Gnomad ASJ AF: 0.000290

Gnomad EAS AF: 0.00109

Gnomad SAS AF: 0.0166

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00323

Gnomad NFE AF: 0.0000899

Gnomad OTH AF: 0.000979

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

GnomAD4 genome AF: 0.000684 AC: 101 AN: 147680 Hom.: 0 Cov.: 28 AF XY: 0.000889 AC XY: 64 AN XY: 71970

Gnomad4 AFR AF: 0.0000492

Gnomad4 AMR AF: 0.000744

Gnomad4 ASJ AF: 0.000290

Gnomad4 EAS AF: 0.00109

Gnomad4 SAS AF: 0.0168

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000899

Gnomad4 OTH AF: 0.000970

Alfa AF: 0.000120 Hom.: 0

Bravo AF: 0.000412

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.11

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1253305; hg19: chr10-99108888;