rs7923749

Variant names:

• chr10-84044676-A-G
• rs7923749
• ENST00000811232.1:n.459-8185T>C

Variant summary

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

The ENST00000811232.1(ENSG00000305475):​n.459-8185T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 152,176 control chromosomes in the GnomAD database, including 8,044 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 0.31 (8044 hom., cov: 32)
• Consequence: ENSG00000305475 ENST00000811232.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.00
• Publications: 1 publications found

Genes affected

ENSG00000305475 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000811232.1. 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
	ENSG00000305475	ENST00000811232.1		n.459-8185T>C		intron	N/A
	ENSG00000305475	ENST00000811233.1		n.420-8185T>C		intron	N/A
	ENSG00000305475	ENST00000811234.1		n.161+4537T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46587 AN: 152058 Hom.: 8022 Cov.: 32

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.307 AC: 46665 AN: 152176 Hom.: 8044 Cov.: 32 AF XY: 0.303 AC XY: 22546 AN XY: 74402

African (AFR) AF: 0.459 AC: 19031 AN: 41494

American (AMR) AF: 0.310 AC: 4734 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1410 AN: 3470

East Asian (EAS) AF: 0.114 AC: 591 AN: 5186

South Asian (SAS) AF: 0.237 AC: 1145 AN: 4828

European-Finnish (FIN) AF: 0.209 AC: 2212 AN: 10602

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16552 AN: 67992

Other (OTH) AF: 0.295 AC: 625 AN: 2116

Alfa AF: 0.278 Hom.: 2408

Bravo AF: 0.318

Asia WGS AF: 0.202 AC: 705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.091
DANN	Benign	0.76
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs7923749; hg19: chr10-85804432;