rs706393

Positions:

• chr1-56185349-T-A
• chr1-56185349-T-C

Variant summary

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

The ENST00000641302.1(ENSG00000260971):​n.323-1729A>T 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 0.0707 in 152,266 control chromosomes in the GnomAD database, including 1,165 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 (1165 hom., cov: 32)
• Consequence: ENST00000641302.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• 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	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000641302.1	n.323-1729A>T		intron_variant, non_coding_transcript_variant
	ENST00000641348.1	n.303-1729A>T		intron_variant, non_coding_transcript_variant
	ENST00000641349.1	n.294-1729A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0705 AC: 10720 AN: 152146 Hom.: 1162 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0274

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0426

Gnomad FIN AF: 0.00198

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00588

Gnomad OTH AF: 0.0631

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

GnomAD4 genome AF: 0.0707 AC: 10759 AN: 152266 Hom.: 1165 Cov.: 32 AF XY: 0.0678 AC XY: 5052 AN XY: 74462

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.0273

Gnomad4 ASJ AF: 0.0164

Gnomad4 EAS AF: 0.000964

Gnomad4 SAS AF: 0.0429

Gnomad4 FIN AF: 0.00198

Gnomad4 NFE AF: 0.00588

Gnomad4 OTH AF: 0.0624

Alfa AF: 0.0115 Hom.: 20

Bravo AF: 0.0790

Asia WGS AF: 0.0360 AC: 123 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.3
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs706393; hg19: chr1-56651021;