rs2256688

Variant names:

• chr10-44768973-A-G
• rs2256688

Your query was ambiguous. Multiple possible variants found:

• chr10-44768973-A-G
• chr10-44768973-A-T

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 0.317 in 152,100 control chromosomes in the GnomAD database, including 8,012 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 0.32 (8012 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.429 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: 0.317 AC: 48229 AN: 151980 Hom.: 7991 Cov.: 33

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.317 AC: 48283 AN: 152100 Hom.: 8012 Cov.: 33 AF XY: 0.316 AC XY: 23496 AN XY: 74372

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.309

Alfa AF: 0.281 Hom.: 7814

Bravo AF: 0.319

Asia WGS AF: 0.235 AC: 815 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2256688; hg19: chr10-45264421;