chr7-82462345-G-A

Variant names:

• chr7-82462345-G-A
• rs10235835
• ENST00000772831.1:n.75-9349G>A

Variant summary

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

The ENST00000772831.1(ENSG00000300590):​n.75-9349G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0279 in 151,140 control chromosomes in the GnomAD database, including 198 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 0.028 (198 hom., cov: 29)
• Consequence: ENSG00000300590 ENST00000772831.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.526
• Publications: 1 publications found

Genes affected

ENSG00000300590 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0924 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000772831.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300590	ENST00000772831.1		n.75-9349G>A		intron	N/A
	ENSG00000300590	ENST00000772832.1		n.66-9349G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0279 AC: 4215 AN: 151032 Hom.: 196 Cov.: 29

Gnomad AFR AF: 0.0949

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0157

Gnomad ASJ AF: 0.00116

Gnomad EAS AF: 0.000779

Gnomad SAS AF: 0.000417

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00641

Gnomad NFE AF: 0.000516

Gnomad OTH AF: 0.0203

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

GnomAD4 genome AF: 0.0279 AC: 4224 AN: 151140 Hom.: 198 Cov.: 29 AF XY: 0.0268 AC XY: 1976 AN XY: 73868

African (AFR) AF: 0.0949 AC: 3897 AN: 41082

American (AMR) AF: 0.0157 AC: 239 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.00116 AC: 4 AN: 3456

East Asian (EAS) AF: 0.000781 AC: 4 AN: 5120

South Asian (SAS) AF: 0.000209 AC: 1 AN: 4788

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10380

Middle Eastern (MID) AF: 0.00690 AC: 2 AN: 290

European-Non Finnish (NFE) AF: 0.000516 AC: 35 AN: 67826

Other (OTH) AF: 0.0201 AC: 42 AN: 2092

Alfa AF: 0.00586 Hom.: 5

Bravo AF: 0.0318

Asia WGS AF: 0.00780 AC: 27 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.23
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs10235835; hg19: chr7-82091661;