rs1449984

chr2-23191780-A-G

Variant summary

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

The NR_171639.1(LOC107985792):n.121+7029T>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 0.261 in 152,146 control chromosomes in the GnomAD database, including 5,533 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 0.26 (5533 hom., cov: 32)
• Consequence: LOC107985792 NR_171639.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

Genes affected

(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 (NFE) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985792	NR_171639.1	n.121+7029T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000669447.1	n.121+7029T>C		intron_variant, non_coding_transcript_variant
	ENST00000440785.1	n.248+7029T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39627 AN: 152028 Hom.: 5535 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.0963

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.261 AC: 39651 AN: 152146 Hom.: 5533 Cov.: 32 AF XY: 0.258 AC XY: 19183 AN XY: 74380

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.0960

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.235

Alfa AF: 0.292 Hom.: 12271

Bravo AF: 0.246

Asia WGS AF: 0.218 AC: 758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	4.0
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1449984; hg19: chr2-23414651;