rs10472818

Variant names:

• chr5-19063960-G-A
• rs10472818
• ENST00000504827.1:n.289+78098C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-19063960-G-A
• chr5-19063960-G-C

Variant summary

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

The ENST00000504827.1(ENSG00000249174):​n.289+78098C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 152,022 control chromosomes in the GnomAD database, including 34,558 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 0.65 (34558 hom., cov: 32)
• Consequence: ENSG00000249174 ENST00000504827.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.75
• Publications: 3 publications found

Genes affected

ENSG00000249174 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000504827.1. 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
	ENSG00000249174	ENST00000504827.1	TSL:3	n.289+78098C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.648 AC: 98468 AN: 151904 Hom.: 34550 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.821

Gnomad FIN AF: 0.764

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.648 AC: 98501 AN: 152022 Hom.: 34558 Cov.: 32 AF XY: 0.658 AC XY: 48933 AN XY: 74346

African (AFR) AF: 0.368 AC: 15235 AN: 41440

American (AMR) AF: 0.769 AC: 11738 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2377 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5157 AN: 5164

South Asian (SAS) AF: 0.820 AC: 3961 AN: 4828

European-Finnish (FIN) AF: 0.764 AC: 8088 AN: 10580

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.730 AC: 49584 AN: 67952

Other (OTH) AF: 0.655 AC: 1385 AN: 2114

Alfa AF: 0.683 Hom.: 6469

Bravo AF: 0.632

Asia WGS AF: 0.894 AC: 3107 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.2
DANN	Benign	0.49
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs10472818; hg19: chr5-19064069;