rs2457401

Positions:

• chr8-79840214-A-G
• chr8-79840214-A-T

Variant summary

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

The NR_110954.1(LOC101927040):​n.303-19699T>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 0.382 in 152,162 control chromosomes in the GnomAD database, including 11,524 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 0.38 (11524 hom., cov: 33)
• Consequence: LOC101927040 NR_110954.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927040	NR_110954.1	n.303-19699T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000502766.2	n.303-19699T>C		intron_variant, non_coding_transcript_variant		2
	ENST00000517365.1	n.192-9633T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.382 AC: 58046 AN: 152046 Hom.: 11507 Cov.: 33

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.382 AC: 58106 AN: 152162 Hom.: 11524 Cov.: 33 AF XY: 0.379 AC XY: 28171 AN XY: 74380

Gnomad4 AFR AF: 0.338

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.455

Gnomad4 NFE AF: 0.427

Gnomad4 OTH AF: 0.407

Alfa AF: 0.290 Hom.: 1049

Bravo AF: 0.371

Asia WGS AF: 0.264 AC: 920 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.2
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2457401; hg19: chr8-80752449;