10-56049270-G-T

Variant names:

• chr10-56049270-G-T
• rs11005196

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 0.0318 in 151,712 control chromosomes in the GnomAD database, including 93 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 0.032 (93 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0318 AC: 4825 AN: 151594 Hom.: 93 Cov.: 32

Gnomad AFR AF: 0.0167

Gnomad AMI AF: 0.00441

Gnomad AMR AF: 0.0365

Gnomad ASJ AF: 0.0880

Gnomad EAS AF: 0.0691

Gnomad SAS AF: 0.0748

Gnomad FIN AF: 0.0388

Gnomad MID AF: 0.0769

Gnomad NFE AF: 0.0299

Gnomad OTH AF: 0.0437

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

GnomAD4 genome AF: 0.0318 AC: 4817 AN: 151712 Hom.: 93 Cov.: 32 AF XY: 0.0334 AC XY: 2479 AN XY: 74126

Gnomad4 AFR AF: 0.0166

Gnomad4 AMR AF: 0.0363

Gnomad4 ASJ AF: 0.0880

Gnomad4 EAS AF: 0.0691

Gnomad4 SAS AF: 0.0747

Gnomad4 FIN AF: 0.0388

Gnomad4 NFE AF: 0.0300

Gnomad4 OTH AF: 0.0433

Alfa AF: 0.0294 Hom.: 53

Bravo AF: 0.0318

Asia WGS AF: 0.0540 AC: 186 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.6
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11005196; hg19: chr10-57809031;