rs6751196

chr2-98750023-G-A

Variant summary

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

The XR_007087150.1(LOC107985922):n.416-1297G>A 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 0.154 in 152,064 control chromosomes in the GnomAD database, including 2,023 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 0.15 (2023 hom., cov: 32)
• Consequence: LOC107985922 XR_007087150.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15

Genes affected

LOC107985922 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985922	XR_007087150.1	n.416-1297G>A		intron_variant, non_coding_transcript_variant
LOC107985922	XR_001739605.2	n.664G>A		non_coding_transcript_exon_variant	1/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23364 AN: 151946 Hom.: 2021 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.0222

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.0802

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.154 AC: 23363 AN: 152064 Hom.: 2023 Cov.: 32 AF XY: 0.150 AC XY: 11142 AN XY: 74358

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.0223

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.0802

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.143

Alfa AF: 0.155 Hom.: 879

Bravo AF: 0.157

Asia WGS AF: 0.129 AC: 447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	5.9
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6751196; hg19: chr2-99366486;