rs1414874

Variant names:

• chr10-83493925-C-A
• rs1414874
• ENST00000846461.1:n.789+23691G>T

Your query was ambiguous. Multiple possible variants found:

• chr10-83493925-C-A
• chr10-83493925-C-G
• chr10-83493925-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000846461.1(ENSG00000309992):​n.789+23691G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.074 in 152,164 control chromosomes in the GnomAD database, including 517 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 0.074 (517 hom., cov: 32)
• Consequence: ENSG00000309992 ENST00000846461.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.282
• Publications: 4 publications found

Genes affected

ENSG00000309992 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.113 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
ENSG00000309992	ENST00000846461.1	n.789+23691G>T		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.0740 AC: 11248 AN: 152048 Hom.: 518 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.0680

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0383

Gnomad FIN AF: 0.0353

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0566

Gnomad OTH AF: 0.0607

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

GnomAD4 genome AF: 0.0740 AC: 11266 AN: 152164 Hom.: 517 Cov.: 32 AF XY: 0.0726 AC XY: 5403 AN XY: 74392

African (AFR) AF: 0.116 AC: 4796 AN: 41482

American (AMR) AF: 0.109 AC: 1670 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0680 AC: 236 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5180

South Asian (SAS) AF: 0.0383 AC: 185 AN: 4826

European-Finnish (FIN) AF: 0.0353 AC: 374 AN: 10608

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0566 AC: 3848 AN: 68010

Other (OTH) AF: 0.0611 AC: 129 AN: 2112

Alfa AF: 0.0723 Hom.: 69

Bravo AF: 0.0809

Asia WGS AF: 0.0300 AC: 105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.2
DANN	Benign	0.64
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1414874; hg19: chr10-85253681;