chr1-55650832-C-T

Position:

• chr1-55650832-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000643167.1(ENSG00000234810):​n.221-22428C>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 0.0283 in 152,322 control chromosomes in the GnomAD database, including 65 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 0.028 (65 hom., cov: 33)
• Consequence: ENST00000643167.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.401

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0283 (4308/152322) while in subpopulation SAS AF= 0.0509 (246/4834). AF 95% confidence interval is 0.0457. There are 65 homozygotes in gnomad4. There are 2145 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 65 gene

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.221-22428C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0283 AC: 4312 AN: 152204 Hom.: 65 Cov.: 33

Gnomad AFR AF: 0.0325

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0263

Gnomad ASJ AF: 0.0469

Gnomad EAS AF: 0.0131

Gnomad SAS AF: 0.0506

Gnomad FIN AF: 0.0268

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0242

Gnomad OTH AF: 0.0402

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

GnomAD4 genome AF: 0.0283 AC: 4308 AN: 152322 Hom.: 65 Cov.: 33 AF XY: 0.0288 AC XY: 2145 AN XY: 74484

Gnomad4 AFR AF: 0.0325

Gnomad4 AMR AF: 0.0262

Gnomad4 ASJ AF: 0.0469

Gnomad4 EAS AF: 0.0131

Gnomad4 SAS AF: 0.0509

Gnomad4 FIN AF: 0.0268

Gnomad4 NFE AF: 0.0242

Gnomad4 OTH AF: 0.0397

Alfa AF: 0.0255 Hom.: 36

Bravo AF: 0.0288

Asia WGS AF: 0.0280 AC: 96 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.8
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72669744; hg19: chr1-56116505;