rs10472818

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000504827.1(ENSG00000249174):​n.289+78098C>T variant causes a intron, non coding transcript 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: ENST00000504827.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.75

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000504827.1	n.289+78098C>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.769

Gnomad4 ASJ AF: 0.685

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.820

Gnomad4 FIN AF: 0.764

Gnomad4 NFE AF: 0.730

Gnomad4 OTH AF: 0.655

Alfa AF: 0.693 Hom.: 6414

Bravo AF: 0.632

Asia WGS AF: 0.894 AC: 3107 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10472818; hg19: chr5-19064069;