rs4972809

Positions:

• chr2-172352363-A-G
• chr2-172352363-A-T

Variant summary

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

The XR_001739773.3(LOC107985960):​n.2666-15408A>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 0.818 in 152,086 control chromosomes in the GnomAD database, including 52,136 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 0.82 (52136 hom., cov: 31)
• Consequence: LOC107985960 XR_001739773.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.960

Genes affected

LOC107985960 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985960	XR_001739773.3	n.2666-15408A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000657632.1	n.239-15408A>G		intron_variant, non_coding_transcript_variant
	ENST00000671082.1	n.862-15408A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.818 AC: 124252 AN: 151968 Hom.: 52108 Cov.: 31

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.899

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.895

Gnomad NFE AF: 0.902

Gnomad OTH AF: 0.828

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

GnomAD4 genome AF: 0.818 AC: 124337 AN: 152086 Hom.: 52136 Cov.: 31 AF XY: 0.807 AC XY: 59986 AN XY: 74320

Gnomad4 AFR AF: 0.767

Gnomad4 AMR AF: 0.810

Gnomad4 ASJ AF: 0.869

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.640

Gnomad4 FIN AF: 0.814

Gnomad4 NFE AF: 0.902

Gnomad4 OTH AF: 0.823

Alfa AF: 0.878 Hom.: 53838

Bravo AF: 0.810

Asia WGS AF: 0.484 AC: 1689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.2
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: rs4972809; hg19: chr2-173217091;