chr1-55523741-T-G

Position:

• chr1-55523741-T-G

Variant summary

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

The ENST00000643167.1(ENSG00000234810):​n.139-91180T>G 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 0.665 in 152,034 control chromosomes in the GnomAD database, including 34,468 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 0.66 (34468 hom., cov: 32)
• Consequence: ENST00000643167.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.742 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
	ENST00000643167.1	n.139-91180T>G		intron_variant, non_coding_transcript_variant
	ENST00000646341.1	n.159-91180T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.665 AC: 101023 AN: 151916 Hom.: 34455 Cov.: 32

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.665 AC: 101079 AN: 152034 Hom.: 34468 Cov.: 32 AF XY: 0.664 AC XY: 49330 AN XY: 74316

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.684

Gnomad4 ASJ AF: 0.728

Gnomad4 EAS AF: 0.578

Gnomad4 SAS AF: 0.548

Gnomad4 FIN AF: 0.783

Gnomad4 NFE AF: 0.747

Gnomad4 OTH AF: 0.653

Alfa AF: 0.669 Hom.: 3793

Bravo AF: 0.651

Asia WGS AF: 0.512 AC: 1780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.25
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs904610; hg19: chr1-55989414;