rs10064219

Variant names:

• chr5-1384883-G-A
• rs10064219
• ENST00000624349.1:n.1527C>T

Variant summary

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

The ENST00000624349.1(ENSG00000279908):​n.1527C>T 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 0.164 in 152,230 control chromosomes in the GnomAD database, including 2,390 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 0.16 (2390 hom., cov: 33)
  • Exomes 𝑓: 0.20 (0 hom.)
• Consequence: ENSG00000279908 ENST00000624349.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240
• Publications: 4 publications found

Genes affected

ENSG00000279908 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.354 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
ENSG00000279908	ENST00000624349.1	n.1527C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24900 AN: 152102 Hom.: 2382 Cov.: 33

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.190

GnomAD4 exome AF: 0.200 AC: 2 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.200 AC XY: 2 AN XY: 10

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 4

Other (OTH) AF: 0.250 AC: 1 AN: 4

GnomAD4 genome AF: 0.164 AC: 24931 AN: 152220 Hom.: 2390 Cov.: 33 AF XY: 0.169 AC XY: 12587 AN XY: 74426

African (AFR) AF: 0.185 AC: 7670 AN: 41508

American (AMR) AF: 0.224 AC: 3421 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 759 AN: 3472

East Asian (EAS) AF: 0.368 AC: 1906 AN: 5176

South Asian (SAS) AF: 0.287 AC: 1386 AN: 4830

European-Finnish (FIN) AF: 0.112 AC: 1189 AN: 10592

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7940 AN: 68026

Other (OTH) AF: 0.196 AC: 415 AN: 2112

Alfa AF: 0.140 Hom.: 1317

Bravo AF: 0.175

Asia WGS AF: 0.339 AC: 1181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.8
DANN	Benign	0.61
PhyloP100		0.024

Splicing

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

Other links and lift over

dbSNP: rs10064219; hg19: chr5-1384998; COSMIC: COSV72961788;