chr7-84875329-T-C

Variant names:

• chr7-84875329-T-C
• rs10499882
• ENST00000804610.1:n.336+4955A>G

Variant summary

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

The ENST00000804610.1(ENSG00000304563):​n.336+4955A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 152,072 control chromosomes in the GnomAD database, including 4,998 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 (4998 hom., cov: 31)
• Consequence: ENSG00000304563 ENST00000804610.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.491
• Publications: 1 publications found

Genes affected

ENSG00000304563 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304563	ENST00000804610.1	n.336+4955A>G		intron_variant	Intron 1 of 1
ENSG00000304563	ENST00000804612.1	n.321+4955A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35517 AN: 151954 Hom.: 4984 Cov.: 31

Gnomad AFR AF: 0.0849

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.234 AC: 35541 AN: 152072 Hom.: 4998 Cov.: 31 AF XY: 0.235 AC XY: 17446 AN XY: 74312

African (AFR) AF: 0.0848 AC: 3519 AN: 41522

American (AMR) AF: 0.316 AC: 4826 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1235 AN: 3472

East Asian (EAS) AF: 0.397 AC: 2040 AN: 5138

South Asian (SAS) AF: 0.339 AC: 1630 AN: 4814

European-Finnish (FIN) AF: 0.224 AC: 2371 AN: 10564

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18954 AN: 67970

Other (OTH) AF: 0.274 AC: 579 AN: 2110

Alfa AF: 0.271 Hom.: 7723

Bravo AF: 0.237

Asia WGS AF: 0.397 AC: 1381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.9
DANN	Benign	0.71
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs10499882; hg19: chr7-84504645;