chr5-64151962-A-G

Variant names:

• chr5-64151962-A-G
• rs356570
• ENST00000845416.1:n.444T>C

Variant summary

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

The ENST00000845416.1(ENSG00000309906):​n.444T>C 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 0.451 in 151,976 control chromosomes in the GnomAD database, including 16,945 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 0.45 (16945 hom., cov: 32)
• Consequence: ENSG00000309906 ENST00000845416.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76
• Publications: 1 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=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 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	ENST00000845416.1	n.444T>C		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000309906	ENST00000845417.1	n.502T>C		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000309906	ENST00000845415.1	n.366-12961T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68513 AN: 151856 Hom.: 16906 Cov.: 32

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.451 AC: 68605 AN: 151976 Hom.: 16945 Cov.: 32 AF XY: 0.442 AC XY: 32815 AN XY: 74268

African (AFR) AF: 0.659 AC: 27285 AN: 41428

American (AMR) AF: 0.403 AC: 6156 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1445 AN: 3468

East Asian (EAS) AF: 0.197 AC: 1017 AN: 5162

South Asian (SAS) AF: 0.360 AC: 1736 AN: 4820

European-Finnish (FIN) AF: 0.280 AC: 2952 AN: 10552

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26418 AN: 67952

Other (OTH) AF: 0.442 AC: 934 AN: 2112

Alfa AF: 0.430 Hom.: 2523

Bravo AF: 0.472

Asia WGS AF: 0.261 AC: 911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.42
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs356570; hg19: chr5-63447789;