1-37317273-A-G

Position:

• chr1-37317273-A-G

Variant summary

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

The ENST00000655056.1(ENSG00000223944):​n.324+1047T>C 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 0.649 in 152,062 control chromosomes in the GnomAD database, including 32,877 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 0.65 (32877 hom., cov: 32)
• Consequence: ENST00000655056.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.941 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
	ENST00000655056.1	n.324+1047T>C		intron_variant, non_coding_transcript_variant
	ENST00000413901.1	n.111+7717T>C		intron_variant, non_coding_transcript_variant		3
	ENST00000702690.1	n.287+1047T>C		intron_variant, non_coding_transcript_variant
	ENST00000702821.1	n.289+1047T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98635 AN: 151944 Hom.: 32862 Cov.: 32

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.963

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.649 AC: 98686 AN: 152062 Hom.: 32877 Cov.: 32 AF XY: 0.655 AC XY: 48738 AN XY: 74376

Gnomad4 AFR AF: 0.520

Gnomad4 AMR AF: 0.748

Gnomad4 ASJ AF: 0.676

Gnomad4 EAS AF: 0.963

Gnomad4 SAS AF: 0.611

Gnomad4 FIN AF: 0.748

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.659

Alfa AF: 0.649 Hom.: 29336

Bravo AF: 0.649

Asia WGS AF: 0.764 AC: 2654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.5
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1411931; hg19: chr1-37782874;