rs16850918

chr4-74319044-A-G

Variant summary

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

The XR_938877.3(LOC105377276):n.272+11154T>C 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 0.0602 in 152,256 control chromosomes in the GnomAD database, including 632 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 0.060 (632 hom., cov: 32)
• Consequence: LOC105377276 XR_938877.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.369

Genes affected

LOC105377276 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377276	XR_938877.3	n.272+11154T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0600 AC: 9126 AN: 152138 Hom.: 629 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0510

Gnomad ASJ AF: 0.00375

Gnomad EAS AF: 0.0532

Gnomad SAS AF: 0.0768

Gnomad FIN AF: 0.00886

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0122

Gnomad OTH AF: 0.0613

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

GnomAD4 genome AF: 0.0602 AC: 9164 AN: 152256 Hom.: 632 Cov.: 32 AF XY: 0.0604 AC XY: 4494 AN XY: 74458

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.0514

Gnomad4 ASJ AF: 0.00375

Gnomad4 EAS AF: 0.0535

Gnomad4 SAS AF: 0.0775

Gnomad4 FIN AF: 0.00886

Gnomad4 NFE AF: 0.0122

Gnomad4 OTH AF: 0.0616

Alfa AF: 0.0307 Hom.: 77

Bravo AF: 0.0673

Asia WGS AF: 0.0900 AC: 312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.8
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16850918; hg19: chr4-75184761;