4-73342482-A-G

Position:

• chr4-73342482-A-G

Variant summary

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

The XR_007058137.1(LOC124900606):​n.1239+771A>G 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 0.407 in 152,008 control chromosomes in the GnomAD database, including 12,982 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 0.41 (12982 hom., cov: 32)
• Consequence: LOC124900606 XR_007058137.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.487

Genes affected

LOC124900606 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124900606	XR_007058137.1	n.1239+771A>G		intron_variant, non_coding_transcript_variant
LOC124900606	XR_007058135.1	n.1237+771A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61872 AN: 151890 Hom.: 12972 Cov.: 32

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.407 AC: 61920 AN: 152008 Hom.: 12982 Cov.: 32 AF XY: 0.413 AC XY: 30656 AN XY: 74298

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.520

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.456

Alfa AF: 0.414 Hom.: 12938

Bravo AF: 0.415

Asia WGS AF: 0.488 AC: 1692 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs714825; hg19: chr4-74208199;