rs4415681

Positions:

• chr10-2344920-G-A
• chr10-2344920-G-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 0.148 in 152,042 control chromosomes in the GnomAD database, including 2,240 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 0.15 (2240 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.694

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.537 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: 0.148 AC: 22560 AN: 151924 Hom.: 2235 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.148 AC: 22577 AN: 152042 Hom.: 2240 Cov.: 32 AF XY: 0.153 AC XY: 11388 AN XY: 74338

Gnomad4 AFR AF: 0.0998

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.554

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.148

Alfa AF: 0.128 Hom.: 1398

Bravo AF: 0.152

Asia WGS AF: 0.313 AC: 1085 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4415681; hg19: chr10-2387114;