rs7920721

Variant names:

• chr10-11678309-A-G
• rs7920721
• ENST00000604086.2:n.123-950A>G

Variant summary

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

The ENST00000833163.1(ENSG00000308311):​n.293+1565T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 152,018 control chromosomes in the GnomAD database, including 8,364 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 (8364 hom., cov: 31)
• Consequence: ENSG00000308311 ENST00000833163.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162
• Publications: 53 publications found

Genes affected

ENSG00000271046 (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 (NFE) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000833163.1. 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
	ENSG00000271046	ENST00000604086.2	TSL:6	n.123-950A>G		intron	N/A
	ENSG00000308311	ENST00000833163.1		n.293+1565T>C		intron	N/A
	ENSG00000308311	ENST00000833164.1		n.293+1565T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47498 AN: 151900 Hom.: 8353 Cov.: 31

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.313 AC: 47520 AN: 152018 Hom.: 8364 Cov.: 31 AF XY: 0.316 AC XY: 23468 AN XY: 74332

African (AFR) AF: 0.153 AC: 6343 AN: 41490

American (AMR) AF: 0.376 AC: 5740 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1461 AN: 3466

East Asian (EAS) AF: 0.239 AC: 1232 AN: 5164

South Asian (SAS) AF: 0.336 AC: 1616 AN: 4814

European-Finnish (FIN) AF: 0.399 AC: 4211 AN: 10546

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.379 AC: 25739 AN: 67960

Other (OTH) AF: 0.342 AC: 721 AN: 2108

Alfa AF: 0.362 Hom.: 7795

Bravo AF: 0.304

Asia WGS AF: 0.274 AC: 951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.0
DANN	Benign	0.38
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs7920721; hg19: chr10-11720308;