rs2812415

Positions:

• chr10-77647212-C-A
• chr10-77647212-C-G
• chr10-77647212-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0022 in 152,162 control chromosomes in the GnomAD database, including 3 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 0.0022 (3 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0022 (334/152162) while in subpopulation EAS AF= 0.032 (165/5162). AF 95% confidence interval is 0.028. There are 3 homozygotes in gnomad4. There are 180 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 3 gene

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: 0.00222 AC: 337 AN: 152044 Hom.: 3 Cov.: 32

Gnomad AFR AF: 0.000386

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00262

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.0325

Gnomad SAS AF: 0.000415

Gnomad FIN AF: 0.000946

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00122

Gnomad OTH AF: 0.00430

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

GnomAD4 genome AF: 0.00220 AC: 334 AN: 152162 Hom.: 3 Cov.: 32 AF XY: 0.00242 AC XY: 180 AN XY: 74386

Gnomad4 AFR AF: 0.000385

Gnomad4 AMR AF: 0.00262

Gnomad4 ASJ AF: 0.00144

Gnomad4 EAS AF: 0.0320

Gnomad4 SAS AF: 0.000415

Gnomad4 FIN AF: 0.000946

Gnomad4 NFE AF: 0.00122

Gnomad4 OTH AF: 0.00425

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.1
DANN	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2812415; hg19: chr10-79406970;