rs10507747

chr13-68371907-T-G

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 0.047 in 152,242 control chromosomes in the GnomAD database, including 490 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 0.047 (490 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.781

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

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: 0.0468 AC: 7115 AN: 152124 Hom.: 484 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0170

Gnomad ASJ AF: 0.0104

Gnomad EAS AF: 0.0125

Gnomad SAS AF: 0.00310

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00526

Gnomad OTH AF: 0.0349

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

GnomAD4 genome AF: 0.0470 AC: 7150 AN: 152242 Hom.: 490 Cov.: 32 AF XY: 0.0455 AC XY: 3385 AN XY: 74430

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.0170

Gnomad4 ASJ AF: 0.0104

Gnomad4 EAS AF: 0.0126

Gnomad4 SAS AF: 0.00311

Gnomad4 FIN AF: 0.00104

Gnomad4 NFE AF: 0.00526

Gnomad4 OTH AF: 0.0341

Alfa AF: 0.0216 Hom.: 35

Bravo AF: 0.0539

Asia WGS AF: 0.0170 AC: 60 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.2
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10507747; hg19: chr13-68946039;