rs7551414

Positions:

• chr1-232856544-T-A

Variant summary

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

The ENST00000667494.1(ENSG00000286774):​n.193-1758T>A 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 0.0148 in 152,318 control chromosomes in the GnomAD database, including 37 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 0.015 (37 hom., cov: 33)
• Consequence: ENST00000667494.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.503

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927711	XR_949278.3	n.796-1758T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000667494.1	n.193-1758T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0147 AC: 2244 AN: 152200 Hom.: 37 Cov.: 33

Gnomad AFR AF: 0.0268

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00811

Gnomad ASJ AF: 0.00807

Gnomad EAS AF: 0.0770

Gnomad SAS AF: 0.0704

Gnomad FIN AF: 0.00235

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00275

Gnomad OTH AF: 0.0119

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

GnomAD4 genome AF: 0.0148 AC: 2251 AN: 152318 Hom.: 37 Cov.: 33 AF XY: 0.0156 AC XY: 1165 AN XY: 74496

Gnomad4 AFR AF: 0.0268

Gnomad4 AMR AF: 0.00810

Gnomad4 ASJ AF: 0.00807

Gnomad4 EAS AF: 0.0774

Gnomad4 SAS AF: 0.0709

Gnomad4 FIN AF: 0.00235

Gnomad4 NFE AF: 0.00275

Gnomad4 OTH AF: 0.0113

Alfa AF: 0.00656 Hom.: 2

Bravo AF: 0.0140

Asia WGS AF: 0.0760 AC: 263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.4
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7551414; hg19: chr1-232992290;