rs1344966

chr10-77774769-T-Cchr10-77774769-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 0.274 in 152,080 control chromosomes in the GnomAD database, including 6,252 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 0.27 (6252 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.403

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.344 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: 0.274 AC: 41704 AN: 151962 Hom.: 6254 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.274 AC: 41689 AN: 152080 Hom.: 6252 Cov.: 32 AF XY: 0.271 AC XY: 20150 AN XY: 74322

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.300

Alfa AF: 0.321 Hom.: 5680

Bravo AF: 0.269

Asia WGS AF: 0.248 AC: 862 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	3.2
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1344966; hg19: chr10-79534527;