10-111600323-C-T

Variant names:

• chr10-111600323-C-T
• rs7077548

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 0.353 in 151,872 control chromosomes in the GnomAD database, including 9,949 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 0.35 (9949 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.500

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.409 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: 0.353 AC: 53638 AN: 151754 Hom.: 9942 Cov.: 31

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.353 AC: 53659 AN: 151872 Hom.: 9949 Cov.: 31 AF XY: 0.353 AC XY: 26226 AN XY: 74232

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.354

Alfa AF: 0.399 Hom.: 24227

Bravo AF: 0.334

Asia WGS AF: 0.256 AC: 892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7077548; hg19: chr10-113360081;