rs4929810

Variant names:

• chr10-123990604-A-G
• rs4929810
• ENST00000830092.1:n.207+5447T>C

Your query was ambiguous. Multiple possible variants found:

• chr10-123990604-A-G
• chr10-123990604-A-T

Variant summary

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

The ENST00000830092.1(ENSG00000307961):​n.207+5447T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.745 in 152,144 control chromosomes in the GnomAD database, including 42,392 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 0.74 (42392 hom., cov: 33)
• Consequence: ENSG00000307961 ENST00000830092.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.525
• Publications: 2 publications found

Genes affected

ENSG00000307961 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000830092.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307961	ENST00000830092.1		n.207+5447T>C		intron	N/A
	ENSG00000307961	ENST00000830093.1		n.276+3860T>C		intron	N/A
	ENSG00000308000	ENST00000830355.1		n.59-366A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.745 AC: 113259 AN: 152026 Hom.: 42363 Cov.: 33

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.755

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

GnomAD4 genome AF: 0.745 AC: 113336 AN: 152144 Hom.: 42392 Cov.: 33 AF XY: 0.741 AC XY: 55140 AN XY: 74372

African (AFR) AF: 0.713 AC: 29568 AN: 41468

American (AMR) AF: 0.765 AC: 11700 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.792 AC: 2750 AN: 3472

East Asian (EAS) AF: 0.615 AC: 3188 AN: 5180

South Asian (SAS) AF: 0.591 AC: 2854 AN: 4830

European-Finnish (FIN) AF: 0.753 AC: 7960 AN: 10576

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.775 AC: 52723 AN: 67998

Other (OTH) AF: 0.753 AC: 1594 AN: 2116

Alfa AF: 0.764 Hom.: 171592

Bravo AF: 0.749

Asia WGS AF: 0.611 AC: 2128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.45
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs4929810; hg19: chr10-125750120;