rs1055144

Positions:

• chr7-25831489-C-T

Variant summary

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

The ENST00000666265.1(ENSG00000286725):​n.215G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 152,128 control chromosomes in the GnomAD database, including 2,914 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 0.17 (2914 hom., cov: 32)
• Consequence: ENST00000666265.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.579

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100506236	XR_108752.5	n.430G>A		non_coding_transcript_exon_variant	3/3
LOC100506236	XR_927110.3	n.368G>A		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000666265.1	n.215G>A		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25754 AN: 152010 Hom.: 2914 Cov.: 32

Gnomad AFR AF: 0.0555

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.169 AC: 25764 AN: 152128 Hom.: 2914 Cov.: 32 AF XY: 0.178 AC XY: 13210 AN XY: 74336

Gnomad4 AFR AF: 0.0554

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.179

Alfa AF: 0.194 Hom.: 4997

Bravo AF: 0.151

Asia WGS AF: 0.369 AC: 1281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.30
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1055144; hg19: chr7-25871109;