rs1819003

chr2-77978776-A-Gchr2-77978776-A-T

Variant summary

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

The NR_110288.1(LOC101927967):n.345-103714T>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 0.858 in 151,264 control chromosomes in the GnomAD database, including 55,756 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 0.86 (55756 hom., cov: 26)
• Consequence: LOC101927967 NR_110288.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.998

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927967	NR_110288.1	n.345-103714T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000667782.1	n.83-38890T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.858 AC: 129615 AN: 151150 Hom.: 55709 Cov.: 26

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.848

Gnomad ASJ AF: 0.844

Gnomad EAS AF: 0.900

Gnomad SAS AF: 0.905

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.865

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

GnomAD4 genome AF: 0.858 AC: 129719 AN: 151264 Hom.: 55756 Cov.: 26 AF XY: 0.862 AC XY: 63611 AN XY: 73832

Gnomad4 AFR AF: 0.914

Gnomad4 AMR AF: 0.848

Gnomad4 ASJ AF: 0.844

Gnomad4 EAS AF: 0.900

Gnomad4 SAS AF: 0.905

Gnomad4 FIN AF: 0.868

Gnomad4 NFE AF: 0.818

Gnomad4 OTH AF: 0.866

Alfa AF: 0.835 Hom.: 6196

Bravo AF: 0.858

Asia WGS AF: 0.922 AC: 3206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.1
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: rs1819003; hg19: chr2-78205902;