rs3123678

Variant names:

• chr10-43620212-T-C
• rs3123678

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 0.513 in 152,046 control chromosomes in the GnomAD database, including 20,646 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 0.51 (20646 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.83

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 = 0.632 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: 0.513 AC: 77953 AN: 151930 Hom.: 20605 Cov.: 32

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.513 AC: 78046 AN: 152046 Hom.: 20646 Cov.: 32 AF XY: 0.512 AC XY: 38008 AN XY: 74306

Gnomad4 AFR AF: 0.639

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.437

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.502

Alfa AF: 0.470 Hom.: 19966

Bravo AF: 0.522

Asia WGS AF: 0.533 AC: 1853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.048
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3123678; hg19: chr10-44115660;