rs2746071

chr1-192808434-A-Gchr1-192808434-A-T

Variant summary

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

The ENST00000644134.1(ENSG00000285280):n.105-42240T>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 0.346 in 152,068 control chromosomes in the GnomAD database, including 9,628 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 0.35 (9628 hom., cov: 32)
• Consequence: ENST00000644134.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.523

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000644134.1	n.105-42240T>C		intron_variant, non_coding_transcript_variant
	ENST00000644058.1	n.194-42240T>C		intron_variant, non_coding_transcript_variant
	ENST00000645822.1	n.200-15966T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52572 AN: 151950 Hom.: 9626 Cov.: 32

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.346 AC: 52603 AN: 152068 Hom.: 9628 Cov.: 32 AF XY: 0.346 AC XY: 25740 AN XY: 74338

Gnomad4 AFR AF: 0.462

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.326

Alfa AF: 0.296 Hom.: 6676

Bravo AF: 0.358

Asia WGS AF: 0.425 AC: 1473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	3.7
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: rs2746071; hg19: chr1-192777564;