5-64157112-T-C

Variant names:

• chr5-64157112-T-C
• rs10036420
• ENST00000845417.1:n.422A>G

Variant summary

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

The ENST00000845417.1(ENSG00000309906):​n.422A>G variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,132 control chromosomes in the GnomAD database, including 2,548 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 0.18 (2548 hom., cov: 32)
• Consequence: ENSG00000309906 ENST00000845417.1 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 4 publications found

Genes affected

ENSG00000309906 (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 (AFR) allele frequency at 95% confidence interval = 0.236 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
ENSG00000309906	ENST00000845417.1	n.422A>G		splice_region_variant, non_coding_transcript_exon_variant	Exon 2 of 3
ENSG00000309906	ENST00000845415.1	n.365+8181A>G		intron_variant	Intron 1 of 3
ENSG00000309906	ENST00000845416.1	n.365-5071A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27095 AN: 152012 Hom.: 2549 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.0998

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.178 AC: 27104 AN: 152132 Hom.: 2548 Cov.: 32 AF XY: 0.173 AC XY: 12893 AN XY: 74376

African (AFR) AF: 0.240 AC: 9962 AN: 41468

American (AMR) AF: 0.174 AC: 2655 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 635 AN: 3472

East Asian (EAS) AF: 0.100 AC: 518 AN: 5170

South Asian (SAS) AF: 0.105 AC: 507 AN: 4816

European-Finnish (FIN) AF: 0.119 AC: 1263 AN: 10602

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10977 AN: 67998

Other (OTH) AF: 0.198 AC: 417 AN: 2102

Alfa AF: 0.161 Hom.: 3169

Bravo AF: 0.187

Asia WGS AF: 0.0940 AC: 328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.3
DANN	Benign	0.41
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs10036420; hg19: chr5-63452939;