rs1426483

Positions:

• chr7-136235882-G-A
• chr7-136235882-G-C
• chr7-136235882-G-T

Variant summary

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

The ENST00000668062.1(ENSG00000232053):​n.115-6268G>A 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 0.683 in 152,076 control chromosomes in the GnomAD database, including 35,726 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 0.68 (35726 hom., cov: 32)
• Consequence: ENST00000668062.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.474

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375523	XR_007060545.1	n.527-6268G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000668062.1	n.115-6268G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.683 AC: 103732 AN: 151958 Hom.: 35686 Cov.: 32

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.703

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

GnomAD4 genome AF: 0.683 AC: 103828 AN: 152076 Hom.: 35726 Cov.: 32 AF XY: 0.682 AC XY: 50665 AN XY: 74322

Gnomad4 AFR AF: 0.700

Gnomad4 AMR AF: 0.725

Gnomad4 ASJ AF: 0.732

Gnomad4 EAS AF: 0.869

Gnomad4 SAS AF: 0.744

Gnomad4 FIN AF: 0.551

Gnomad4 NFE AF: 0.661

Gnomad4 OTH AF: 0.707

Alfa AF: 0.674 Hom.: 45223

Bravo AF: 0.700

Asia WGS AF: 0.825 AC: 2869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.36
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1426483; hg19: chr7-135920630;