7-75722-C-T

Position:

• chr7-75722-C-T

Variant summary

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

The XR_007060630.1(LOC105375113):​n.1242G>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 0.283 in 150,716 control chromosomes in the GnomAD database, including 3,614 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 0.28 (3614 hom., cov: 33)
• Consequence: LOC105375113 XR_007060630.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140

Genes affected

LOC105375113 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375113	XR_007060630.1	n.1242G>A		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000465755.2	n.121-3889G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42689 AN: 150614 Hom.: 3614 Cov.: 33

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.352

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.283 AC: 42700 AN: 150716 Hom.: 3614 Cov.: 33 AF XY: 0.284 AC XY: 20898 AN XY: 73682

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.360

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.306

Alfa AF: 0.178 Hom.: 208

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10233991; hg19: chr7-75722;