rs720428

Positions:

• chr4-56690636-A-G
• chr4-56690636-A-T

Variant summary

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

The XR_941078.3(LOC105377666):​n.314-5539A>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 0.574 in 152,038 control chromosomes in the GnomAD database, including 25,977 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 0.57 (25977 hom., cov: 32)
• Consequence: LOC105377666 XR_941078.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590

Genes affected

LOC105377666 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377666	XR_941078.3	n.314-5539A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87166 AN: 151920 Hom.: 25965 Cov.: 32

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.574 AC: 87220 AN: 152038 Hom.: 25977 Cov.: 32 AF XY: 0.576 AC XY: 42838 AN XY: 74328

Gnomad4 AFR AF: 0.407

Gnomad4 AMR AF: 0.586

Gnomad4 ASJ AF: 0.652

Gnomad4 EAS AF: 0.655

Gnomad4 SAS AF: 0.620

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.645

Gnomad4 OTH AF: 0.561

Alfa AF: 0.600 Hom.: 3450

Bravo AF: 0.562

Asia WGS AF: 0.613 AC: 2136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.5
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs720428; hg19: chr4-57556802;