rs4415681

Variant names:

• chr10-2344920-G-A
• rs4415681

Your query was ambiguous. Multiple possible variants found:

• chr10-2344920-G-A
• chr10-2344920-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0998 AC: 4140 AN: 41474

American (AMR) AF: 0.210 AC: 3204 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 610 AN: 3472

East Asian (EAS) AF: 0.554 AC: 2861 AN: 5168

South Asian (SAS) AF: 0.185 AC: 894 AN: 4820

European-Finnish (FIN) AF: 0.156 AC: 1652 AN: 10564

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8739 AN: 67980

Other (OTH) AF: 0.148 AC: 312 AN: 2104

Alfa AF: 0.130 Hom.: 1916

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
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs4415681; hg19: chr10-2387114;