8-67344653-A-T

Variant names:

• chr8-67344653-A-T
• rs718348
• ENST00000607397.1:n.679A>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000607397.1(ARFGEF1-DT):​n.679A>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 0.334 in 152,088 control chromosomes in the GnomAD database, including 8,779 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 0.33 (8779 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: ARFGEF1-DT ENST00000607397.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136

Genes affected

ARFGEF1-DT (HGNC:55237): (ARFGEF1 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARFGEF1-DT	NR_136223.1	n.469+351A>T		intron_variant	Intron 1 of 2
ARFGEF1-DT	NR_136224.1	n.469+351A>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARFGEF1-DT	ENST00000607397.1	n.679A>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50665 AN: 151962 Hom.: 8764 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.311

GnomAD4 exome AF: 0.500 AC: 4 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.334 AC: 50726 AN: 152080 Hom.: 8779 Cov.: 32 AF XY: 0.335 AC XY: 24923 AN XY: 74336

Gnomad4 AFR AF: 0.414

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.397

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.313

Alfa AF: 0.316 Hom.: 939

Bravo AF: 0.336

Asia WGS AF: 0.359 AC: 1247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.9
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs718348; hg19: chr8-68256888;