rs3103190

chr4-42320929-G-A

Variant summary

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

The NR_134668.1(LOC105374428):n.95-21618C>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 0.683 in 152,182 control chromosomes in the GnomAD database, including 35,649 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 0.68 (35649 hom., cov: 34)
• Consequence: LOC105374428 NR_134668.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

Genes affected

(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 = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374428	NR_134668.1	n.95-21618C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000503321.1	n.60-37538C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000508911.1	n.95-21618C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.683 AC: 103917 AN: 152064 Hom.: 35634 Cov.: 34

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.683 AC: 103971 AN: 152182 Hom.: 35649 Cov.: 34 AF XY: 0.689 AC XY: 51280 AN XY: 74388

Gnomad4 AFR AF: 0.679

Gnomad4 AMR AF: 0.750

Gnomad4 ASJ AF: 0.764

Gnomad4 EAS AF: 0.691

Gnomad4 SAS AF: 0.654

Gnomad4 FIN AF: 0.733

Gnomad4 NFE AF: 0.662

Gnomad4 OTH AF: 0.709

Alfa AF: 0.675 Hom.: 41268

Bravo AF: 0.685

Asia WGS AF: 0.676 AC: 2349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.0
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3103190; hg19: chr4-42322946;