rs11677200

Positions:

• chr2-151354129-T-C
• chr2-151354129-T-G

Variant summary

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

The NR_110248.1(LOC101929319):​n.307-14730A>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 0.34 in 152,010 control chromosomes in the GnomAD database, including 9,947 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 0.34 (9947 hom., cov: 31)
• Consequence: LOC101929319 NR_110248.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.547

Genes affected

LOC101929319 (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 = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101929319	NR_110248.1	n.307-14730A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51721 AN: 151892 Hom.: 9941 Cov.: 31

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.340 AC: 51720 AN: 152010 Hom.: 9947 Cov.: 31 AF XY: 0.346 AC XY: 25717 AN XY: 74300

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.345

Alfa AF: 0.374 Hom.: 1901

Bravo AF: 0.340

Asia WGS AF: 0.342 AC: 1189 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	0.95
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11677200; hg19: chr2-152210643;