rs7234864

Variant names:

• chr18-60067625-C-T
• rs7234864
• ENST00000810803.1:n.745G>A

Variant summary

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

The ENST00000810803.1(ENSG00000305409):​n.745G>A 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 0.313 in 152,024 control chromosomes in the GnomAD database, including 8,413 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 0.31 (8413 hom., cov: 32)
• Consequence: ENSG00000305409 ENST00000810803.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.00
• Publications: 28 publications found

Genes affected

ENSG00000305409 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.475 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
ENSG00000305409	ENST00000810803.1	n.745G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47496 AN: 151906 Hom.: 8401 Cov.: 32

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.313 AC: 47560 AN: 152024 Hom.: 8413 Cov.: 32 AF XY: 0.308 AC XY: 22857 AN XY: 74318

African (AFR) AF: 0.480 AC: 19914 AN: 41460

American (AMR) AF: 0.211 AC: 3216 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 866 AN: 3470

East Asian (EAS) AF: 0.167 AC: 862 AN: 5160

South Asian (SAS) AF: 0.350 AC: 1683 AN: 4812

European-Finnish (FIN) AF: 0.180 AC: 1898 AN: 10556

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18089 AN: 67978

Other (OTH) AF: 0.302 AC: 638 AN: 2112

Alfa AF: 0.279 Hom.: 25028

Bravo AF: 0.321

Asia WGS AF: 0.232 AC: 805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.047
DANN	Benign	0.56
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs7234864; hg19: chr18-57734857;