rs7068990

Variant names:

• chr10-120329400-G-A
• rs7068990
• ENST00000794040.1:n.277-7121G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-120329400-G-A
• chr10-120329400-G-C

Variant summary

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

The ENST00000794040.1(ENSG00000303377):​n.277-7121G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 151,178 control chromosomes in the GnomAD database, including 4,299 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 0.23 (4299 hom., cov: 31)
• Consequence: ENSG00000303377 ENST00000794040.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306
• Publications: 2 publications found

Genes affected

ENSG00000303377 (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000794040.1. 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
	ENSG00000303377	ENST00000794040.1		n.277-7121G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34544 AN: 151062 Hom.: 4295 Cov.: 31

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.229 AC: 34555 AN: 151178 Hom.: 4299 Cov.: 31 AF XY: 0.237 AC XY: 17551 AN XY: 73926

African (AFR) AF: 0.187 AC: 7591 AN: 40640

American (AMR) AF: 0.165 AC: 2520 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 878 AN: 3466

East Asian (EAS) AF: 0.253 AC: 1306 AN: 5160

South Asian (SAS) AF: 0.335 AC: 1615 AN: 4816

European-Finnish (FIN) AF: 0.406 AC: 4288 AN: 10566

Middle Eastern (MID) AF: 0.0822 AC: 24 AN: 292

European-Non Finnish (NFE) AF: 0.229 AC: 15538 AN: 67960

Other (OTH) AF: 0.221 AC: 464 AN: 2104

Alfa AF: 0.230 Hom.: 3135

Bravo AF: 0.205

Asia WGS AF: 0.291 AC: 1009 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.34
PhyloP100		0.31

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7068990;

hg19: chr10-122088912;