chr4-80248758-G-T

Position:

• chr4-80248758-G-T

Variant summary

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

The XR_007058161.1(LOC124900725):​n.81-6607G>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 0.234 in 151,978 control chromosomes in the GnomAD database, including 5,137 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 0.23 (5137 hom., cov: 32)
• Consequence: LOC124900725 XR_007058161.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194

Genes affected

LOC124900725 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124900725	XR_007058161.1	n.81-6607G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35599 AN: 151860 Hom.: 5138 Cov.: 32

Gnomad AFR AF: 0.0691

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.234 AC: 35595 AN: 151978 Hom.: 5137 Cov.: 32 AF XY: 0.236 AC XY: 17524 AN XY: 74254

Gnomad4 AFR AF: 0.0689

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.240

Gnomad4 EAS AF: 0.417

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.229

Alfa AF: 0.168 Hom.: 424

Bravo AF: 0.222

Asia WGS AF: 0.320 AC: 1114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.2
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11099098; hg19: chr4-81169912;