7-155312071-G-T

Variant names:

• chr7-155312071-G-T
• rs13223383
• XR_007060611.1:n.1266C>A

Variant summary

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

The XR_007060611.1(LOC105375592):​n.1266C>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 0.688 in 152,132 control chromosomes in the GnomAD database, including 36,582 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 0.69 (36582 hom., cov: 33)
• Consequence: LOC105375592 XR_007060611.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.501

Genes affected

LOC105375592 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375592	XR_007060611.1	n.1266C>A		non_coding_transcript_exon_variant	Exon 2 of 2
LOC105375592	XR_007060612.1	n.1313C>A		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.688 AC: 104535 AN: 152014 Hom.: 36540 Cov.: 33

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.856

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.688 AC: 104626 AN: 152132 Hom.: 36582 Cov.: 33 AF XY: 0.681 AC XY: 50618 AN XY: 74350

Gnomad4 AFR AF: 0.726

Gnomad4 AMR AF: 0.689

Gnomad4 ASJ AF: 0.606

Gnomad4 EAS AF: 0.313

Gnomad4 SAS AF: 0.503

Gnomad4 FIN AF: 0.657

Gnomad4 NFE AF: 0.713

Gnomad4 OTH AF: 0.687

Alfa AF: 0.700 Hom.: 76862

Bravo AF: 0.694

Asia WGS AF: 0.480 AC: 1667 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.1
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13223383; hg19: chr7-155103781;