rs10504672

Variant names:

• chr8-78082964-G-C
• rs10504672
• ENST00000810365.1:n.437+5707G>C

Your query was ambiguous. Multiple possible variants found:

• chr8-78082964-G-C
• chr8-78082964-G-T

Variant summary

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

The ENST00000810365.1(ENSG00000305312):​n.437+5707G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 151,850 control chromosomes in the GnomAD database, including 15,851 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 0.44 (15851 hom., cov: 32)
• Consequence: ENSG00000305312 ENST00000810365.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136
• Publications: 0 publications found

Genes affected

ENSG00000305312 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.623 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
ENSG00000305312	ENST00000810365.1	n.437+5707G>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66600 AN: 151732 Hom.: 15821 Cov.: 32

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.439 AC: 66681 AN: 151850 Hom.: 15851 Cov.: 32 AF XY: 0.436 AC XY: 32367 AN XY: 74190

African (AFR) AF: 0.629 AC: 26079 AN: 41432

American (AMR) AF: 0.404 AC: 6155 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1384 AN: 3472

East Asian (EAS) AF: 0.500 AC: 2556 AN: 5112

South Asian (SAS) AF: 0.458 AC: 2212 AN: 4826

European-Finnish (FIN) AF: 0.323 AC: 3411 AN: 10550

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23395 AN: 67894

Other (OTH) AF: 0.430 AC: 909 AN: 2112

Alfa AF: 0.239 Hom.: 533

Bravo AF: 0.456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	10
DANN	Benign	0.67
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs10504672; hg19: chr8-78995199;