1-224823940-A-G

Position:

• chr1-224823940-A-G

Variant summary

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

The ENST00000657178.1(ENSG00000286719):​n.78-2952T>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 0.915 in 152,260 control chromosomes in the GnomAD database, including 63,919 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 0.91 (63919 hom., cov: 32)
• Consequence: ENST00000657178.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.863

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.953 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
	ENST00000657178.1	n.78-2952T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.915 AC: 139135 AN: 152142 Hom.: 63865 Cov.: 32

Gnomad AFR AF: 0.961

Gnomad AMI AF: 0.891

Gnomad AMR AF: 0.835

Gnomad ASJ AF: 0.927

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.923

Gnomad OTH AF: 0.912

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

GnomAD4 genome AF: 0.915 AC: 139248 AN: 152260 Hom.: 63919 Cov.: 32 AF XY: 0.909 AC XY: 67692 AN XY: 74434

Gnomad4 AFR AF: 0.961

Gnomad4 AMR AF: 0.835

Gnomad4 ASJ AF: 0.927

Gnomad4 EAS AF: 0.763

Gnomad4 SAS AF: 0.809

Gnomad4 FIN AF: 0.910

Gnomad4 NFE AF: 0.923

Gnomad4 OTH AF: 0.912

Alfa AF: 0.901 Hom.: 5718

Bravo AF: 0.911

Asia WGS AF: 0.794 AC: 2759 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.0060
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2662928; hg19: chr1-225011642;