7-134641192-A-T

Variant names:

• chr7-134641192-A-T
• rs1424445
• XR_007060537.1:n.29222-21244T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007060537.1(LOC124901750):​n.29222-21244T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 151,916 control chromosomes in the GnomAD database, including 26,843 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 0.58 (26843 hom., cov: 31)
• Consequence: LOC124901750 XR_007060537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.717
• Publications: 5 publications found

Genes affected

LOC124901750 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901750	XR_007060537.1	n.29222-21244T>A		intron_variant	Intron 1 of 1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88520 AN: 151798 Hom.: 26819 Cov.: 31

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.719

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.583 AC: 88602 AN: 151916 Hom.: 26843 Cov.: 31 AF XY: 0.590 AC XY: 43795 AN XY: 74286

African (AFR) AF: 0.711 AC: 29456 AN: 41440

American (AMR) AF: 0.563 AC: 8584 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1758 AN: 3466

East Asian (EAS) AF: 0.888 AC: 4579 AN: 5154

South Asian (SAS) AF: 0.718 AC: 3461 AN: 4820

European-Finnish (FIN) AF: 0.532 AC: 5621 AN: 10558

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.491 AC: 33360 AN: 67906

Other (OTH) AF: 0.552 AC: 1164 AN: 2110

Alfa AF: 0.524 Hom.: 2690

Bravo AF: 0.589

Asia WGS AF: 0.763 AC: 2649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.2
DANN	Benign	0.44
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs1424445; hg19: chr7-134325944;