rs994960

Positions:

• chr3-73682765-G-A
• chr3-73682765-G-C
• chr3-73682765-G-T

Variant summary

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

The XR_001740755.1(LOC105377164):​n.351-4340C>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 0.415 in 151,948 control chromosomes in the GnomAD database, including 14,717 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 0.41 (14717 hom., cov: 31)
• Consequence: LOC105377164 XR_001740755.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.957

Genes affected

LOC105377164 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377164	XR_001740755.1	n.351-4340C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.415 AC: 62994 AN: 151830 Hom.: 14711 Cov.: 31

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.415 AC: 63007 AN: 151948 Hom.: 14717 Cov.: 31 AF XY: 0.416 AC XY: 30912 AN XY: 74274

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.559

Gnomad4 SAS AF: 0.492

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.420

Alfa AF: 0.351 Hom.: 1722

Bravo AF: 0.400

Asia WGS AF: 0.498 AC: 1731 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.2
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs994960; hg19: chr3-73731916;