rs576523

chr1-160776286-G-Achr1-160776286-G-Cchr1-160776286-G-T

Variant summary

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

The ENST00000620690.1(ENSG00000275801):n.262+61C>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 0.923 in 152,278 control chromosomes in the GnomAD database, including 65,859 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 0.92 (65831 hom., cov: 32)
  • Exomes 𝑓: 1.0 (28 hom.)
• Consequence: ENST00000620690.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.464

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.991 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371470	XR_001738267.2	n.455+33C>T		intron_variant, non_coding_transcript_variant
LOC105371470	XR_007066688.1	n.447C>T		non_coding_transcript_exon_variant	2/2
LOC105371470	XR_922205.3	n.414+33C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000620690.1	n.262+61C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.923 AC: 140401 AN: 152104 Hom.: 65808 Cov.: 32

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.985

Gnomad AMR AF: 0.967

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.997

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.997

Gnomad OTH AF: 0.942

GnomAD4 exome AF: 1.00 AC: 56 AN: 56 Hom.: 28 Cov.: 0 AF XY: 1.00 AC XY: 48 AN XY: 48

Gnomad4 AFR exome AF: 1.00

Gnomad4 ASJ exome AF: 1.00

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.923 AC: 140475 AN: 152222 Hom.: 65831 Cov.: 32 AF XY: 0.925 AC XY: 68850 AN XY: 74428

Gnomad4 AFR AF: 0.737

Gnomad4 AMR AF: 0.968

Gnomad4 ASJ AF: 1.00

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.997

Gnomad4 FIN AF: 0.999

Gnomad4 NFE AF: 0.997

Gnomad4 OTH AF: 0.942

Alfa AF: 0.974 Hom.: 16803

Bravo AF: 0.913

Asia WGS AF: 0.982 AC: 3416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.90
Dann	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs576523; hg19: chr1-160746076;