rs10474433

Variant names:

• chr5-75321018-T-C
• rs10474433
• ENST00000792193.1:n.103A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-75321018-T-C
• chr5-75321018-T-G

Variant summary

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

The ENST00000792193.1(ENSG00000247372):​n.103A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 152,070 control chromosomes in the GnomAD database, including 10,087 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 0.36 (10087 hom., cov: 33)
• Consequence: ENSG00000247372 ENST00000792193.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.616
• Publications: 13 publications found

Genes affected

ENSG00000247372 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000792193.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000247372	ENST00000792193.1		n.103A>G		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000247372	ENST00000792194.1		n.98A>G		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000247372	ENST00000501886.2	TSL:4	n.199-535A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55104 AN: 151952 Hom.: 10078 Cov.: 33

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.363 AC: 55145 AN: 152070 Hom.: 10087 Cov.: 33 AF XY: 0.366 AC XY: 27234 AN XY: 74352

African (AFR) AF: 0.368 AC: 15283 AN: 41478

American (AMR) AF: 0.354 AC: 5411 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1639 AN: 3470

East Asian (EAS) AF: 0.321 AC: 1655 AN: 5152

South Asian (SAS) AF: 0.555 AC: 2677 AN: 4824

European-Finnish (FIN) AF: 0.356 AC: 3759 AN: 10570

Middle Eastern (MID) AF: 0.384 AC: 112 AN: 292

European-Non Finnish (NFE) AF: 0.346 AC: 23515 AN: 67974

Other (OTH) AF: 0.367 AC: 775 AN: 2110

Alfa AF: 0.356 Hom.: 42712

Bravo AF: 0.356

Asia WGS AF: 0.423 AC: 1471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.3
DANN	Benign	0.73
PhyloP100		-0.62

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10474433;

hg19: chr5-74616843;