rs706394

chr1-56183430-G-C

Variant summary

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

The ENST00000641302.1(ENSG00000260971):n.448+65C>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0706 in 152,128 control chromosomes in the GnomAD database, including 1,167 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 0.071 (1167 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENST00000641302.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000641302.1	n.448+65C>G		intron_variant, non_coding_transcript_variant
	ENST00000641348.1	n.428+65C>G		intron_variant, non_coding_transcript_variant
	ENST00000641349.1	n.419+65C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0704 AC: 10706 AN: 152010 Hom.: 1164 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0275

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.000965

Gnomad SAS AF: 0.0429

Gnomad FIN AF: 0.00189

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00591

Gnomad OTH AF: 0.0630

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 12 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 12

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0706 AC: 10742 AN: 152128 Hom.: 1167 Cov.: 32 AF XY: 0.0678 AC XY: 5047 AN XY: 74400

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.0274

Gnomad4 ASJ AF: 0.0164

Gnomad4 EAS AF: 0.000967

Gnomad4 SAS AF: 0.0429

Gnomad4 FIN AF: 0.00189

Gnomad4 NFE AF: 0.00591

Gnomad4 OTH AF: 0.0624

Alfa AF: 0.0429 Hom.: 94

Bravo AF: 0.0789

Asia WGS AF: 0.0370 AC: 128 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	1.8
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs706394; hg19: chr1-56649102;