chr4-156142163-G-C

Position:

• chr4-156142163-G-C

Variant summary

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

The XR_427618.3(LOC102724785):​n.123+1589C>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 0.841 in 152,128 control chromosomes in the GnomAD database, including 54,146 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 0.84 (54146 hom., cov: 32)
• Consequence: LOC102724785 XR_427618.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.837

Genes affected

LOC102724785 (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 (NFE) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102724785	XR_427618.3	n.123+1589C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.842 AC: 127921 AN: 152010 Hom.: 54110 Cov.: 32

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.912

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.831

Gnomad EAS AF: 0.866

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.882

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.888

Gnomad OTH AF: 0.847

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

GnomAD4 genome AF: 0.841 AC: 128000 AN: 152128 Hom.: 54146 Cov.: 32 AF XY: 0.837 AC XY: 62249 AN XY: 74368

Gnomad4 AFR AF: 0.797

Gnomad4 AMR AF: 0.729

Gnomad4 ASJ AF: 0.831

Gnomad4 EAS AF: 0.867

Gnomad4 SAS AF: 0.792

Gnomad4 FIN AF: 0.882

Gnomad4 NFE AF: 0.888

Gnomad4 OTH AF: 0.846

Alfa AF: 0.864 Hom.: 6732

Bravo AF: 0.832

Asia WGS AF: 0.838 AC: 2915 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.67
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7670748; hg19: chr4-157063315;