rs2116422

Positions:

• chr8-97250016-G-A

Variant summary

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

The NR_125390.1(LOC101927066):​n.471+169054C>T 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 0.167 in 152,122 control chromosomes in the GnomAD database, including 3,081 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 0.17 (3081 hom., cov: 33)
• Consequence: LOC101927066 NR_125390.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108

Genes affected

LOC101927066 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927066	NR_125390.1	n.471+169054C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25461 AN: 152004 Hom.: 3087 Cov.: 33

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.0594

Gnomad EAS AF: 0.0981

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.0982

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.167 AC: 25471 AN: 152122 Hom.: 3081 Cov.: 33 AF XY: 0.163 AC XY: 12159 AN XY: 74384

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.0594

Gnomad4 EAS AF: 0.0974

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.0982

Gnomad4 OTH AF: 0.135

Alfa AF: 0.109 Hom.: 1456

Bravo AF: 0.179

Asia WGS AF: 0.123 AC: 427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.27
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2116422; hg19: chr8-98262244;