rs6972823

chr7-3196264-T-A

Variant summary

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

The XR_007060192.1(LOC124901574):n.1057A>T 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 0.636 in 152,014 control chromosomes in the GnomAD database, including 31,274 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 0.64 (31274 hom., cov: 32)
• Consequence: LOC124901574 XR_007060192.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520

Genes affected

LOC124901574 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901574	XR_007060192.1	n.1057A>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96555 AN: 151896 Hom.: 31240 Cov.: 32

Gnomad AFR AF: 0.759

Gnomad AMI AF: 0.650

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.526

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.636 AC: 96640 AN: 152014 Hom.: 31274 Cov.: 32 AF XY: 0.635 AC XY: 47202 AN XY: 74292

Gnomad4 AFR AF: 0.759

Gnomad4 AMR AF: 0.629

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.649

Gnomad4 SAS AF: 0.500

Gnomad4 FIN AF: 0.635

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.614

Alfa AF: 0.612 Hom.: 3564

Bravo AF: 0.640

Asia WGS AF: 0.630 AC: 2192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.4
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: rs6972823; hg19: chr7-3235896;