rs16850885

chr4-74304423-G-A

Variant summary

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

The XR_938877.3(LOC105377276):n.273-25645C>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 0.0606 in 152,182 control chromosomes in the GnomAD database, including 642 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 0.061 (642 hom., cov: 32)
• Consequence: LOC105377276 XR_938877.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.389

Genes affected

LOC105377276 (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 (AFR) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377276	XR_938877.3	n.273-25645C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0604 AC: 9178 AN: 152064 Hom.: 639 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0505

Gnomad ASJ AF: 0.00374

Gnomad EAS AF: 0.0528

Gnomad SAS AF: 0.0775

Gnomad FIN AF: 0.00952

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0122

Gnomad OTH AF: 0.0593

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

GnomAD4 genome AF: 0.0606 AC: 9216 AN: 152182 Hom.: 642 Cov.: 32 AF XY: 0.0606 AC XY: 4508 AN XY: 74410

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.0509

Gnomad4 ASJ AF: 0.00374

Gnomad4 EAS AF: 0.0531

Gnomad4 SAS AF: 0.0782

Gnomad4 FIN AF: 0.00952

Gnomad4 NFE AF: 0.0122

Gnomad4 OTH AF: 0.0597

Alfa AF: 0.0218 Hom.: 225

Bravo AF: 0.0674

Asia WGS AF: 0.0910 AC: 314 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	0.94
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16850885; hg19: chr4-75170140;