7-4474175-C-T

Position:

• chr7-4474175-C-T

Variant summary

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

The XR_007060198.1(LOC124901579):​n.46-1985C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 151,754 control chromosomes in the GnomAD database, including 21,630 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 0.53 (21630 hom., cov: 31)
• Consequence: LOC124901579 XR_007060198.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87

Genes affected

LOC124901579 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901579	XR_007060198.1	n.46-1985C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.533 AC: 80812 AN: 151638 Hom.: 21602 Cov.: 31

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.689

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.533 AC: 80878 AN: 151754 Hom.: 21630 Cov.: 31 AF XY: 0.536 AC XY: 39699 AN XY: 74126

Gnomad4 AFR AF: 0.515

Gnomad4 AMR AF: 0.591

Gnomad4 ASJ AF: 0.541

Gnomad4 EAS AF: 0.688

Gnomad4 SAS AF: 0.563

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.536

Alfa AF: 0.524 Hom.: 11128

Bravo AF: 0.541

Asia WGS AF: 0.587 AC: 2042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.20
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4720301; hg19: chr7-4513806;