10-84260944-T-C

Variant names:

• chr10-84260944-T-C
• rs4244950

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.471 in 152,156 control chromosomes in the GnomAD database, including 18,854 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 0.47 (18854 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.715 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: 0.471 AC: 71594 AN: 152038 Hom.: 18827 Cov.: 33

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.471 AC: 71656 AN: 152156 Hom.: 18854 Cov.: 33 AF XY: 0.472 AC XY: 35078 AN XY: 74368

African (AFR) AF: 0.722 AC: 29978 AN: 41506

American (AMR) AF: 0.430 AC: 6566 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1096 AN: 3470

East Asian (EAS) AF: 0.338 AC: 1745 AN: 5168

South Asian (SAS) AF: 0.332 AC: 1603 AN: 4828

European-Finnish (FIN) AF: 0.465 AC: 4920 AN: 10582

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.358 AC: 24355 AN: 68000

Other (OTH) AF: 0.430 AC: 908 AN: 2114

Alfa AF: 0.381 Hom.: 23290

Bravo AF: 0.480

Asia WGS AF: 0.370 AC: 1287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.2
DANN	Benign	0.62
PhyloP100		0.070

Splicing

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

Other links and lift over

dbSNP: rs4244950; hg19: chr10-86020700;