rs524991

Positions:

• chr1-60864031-G-A

Variant summary

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

The ENST00000667362.1(ENSG00000231252):​n.93+3886C>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 0.0501 in 152,142 control chromosomes in the GnomAD database, including 259 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 0.050 (259 hom., cov: 32)
• Consequence: ENST00000667362.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0849 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
	ENST00000667362.1	n.93+3886C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0502 AC: 7628 AN: 152024 Hom.: 260 Cov.: 32

Gnomad AFR AF: 0.0149

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0889

Gnomad ASJ AF: 0.0637

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.0297

Gnomad FIN AF: 0.0341

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0703

Gnomad OTH AF: 0.0543

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

GnomAD4 genome AF: 0.0501 AC: 7625 AN: 152142 Hom.: 259 Cov.: 32 AF XY: 0.0486 AC XY: 3613 AN XY: 74372

Gnomad4 AFR AF: 0.0148

Gnomad4 AMR AF: 0.0889

Gnomad4 ASJ AF: 0.0637

Gnomad4 EAS AF: 0.00270

Gnomad4 SAS AF: 0.0297

Gnomad4 FIN AF: 0.0341

Gnomad4 NFE AF: 0.0702

Gnomad4 OTH AF: 0.0528

Alfa AF: 0.0510 Hom.: 29

Bravo AF: 0.0547

Asia WGS AF: 0.0200 AC: 69 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.6
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs524991; hg19: chr1-61329703;