rs1404697

Positions:

• chr7-108904404-G-C

Variant summary

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

The ENST00000623718.1(ENSG00000279043):​n.823C>G 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 0.0534 in 152,236 control chromosomes in the GnomAD database, including 248 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 0.053 (248 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENST00000623718.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000623718.1	n.823C>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0534 AC: 8128 AN: 152120 Hom.: 249 Cov.: 32

Gnomad AFR AF: 0.0460

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0393

Gnomad ASJ AF: 0.0193

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.0706

Gnomad FIN AF: 0.0474

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0558

Gnomad OTH AF: 0.0503

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 16 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 10

Gnomad4 ASJ exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0534 AC: 8125 AN: 152236 Hom.: 248 Cov.: 32 AF XY: 0.0532 AC XY: 3963 AN XY: 74438

Gnomad4 AFR AF: 0.0459

Gnomad4 AMR AF: 0.0395

Gnomad4 ASJ AF: 0.0193

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.0711

Gnomad4 FIN AF: 0.0474

Gnomad4 NFE AF: 0.0558

Gnomad4 OTH AF: 0.0493

Alfa AF: 0.0574 Hom.: 162

Bravo AF: 0.0517

Asia WGS AF: 0.108 AC: 375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.94
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1404697; hg19: chr7-108544461;