rs6744978

Positions:

• chr2-191188980-C-A

Variant summary

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

The XR_923707.3(LOC105373804):​n.127+10984C>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 0.145 in 152,126 control chromosomes in the GnomAD database, including 4,946 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 0.14 (4946 hom., cov: 32)
• Consequence: LOC105373804 XR_923707.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442

Genes affected

LOC105373804 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373804	XR_923707.3	n.127+10984C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.145 AC: 21970 AN: 152008 Hom.: 4931 Cov.: 32

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0584

Gnomad ASJ AF: 0.0256

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.0122

Gnomad FIN AF: 0.00132

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0112

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.145 AC: 22023 AN: 152126 Hom.: 4946 Cov.: 32 AF XY: 0.139 AC XY: 10301 AN XY: 74366

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.0583

Gnomad4 ASJ AF: 0.0256

Gnomad4 EAS AF: 0.00309

Gnomad4 SAS AF: 0.0122

Gnomad4 FIN AF: 0.00132

Gnomad4 NFE AF: 0.0112

Gnomad4 OTH AF: 0.119

Alfa AF: 0.0462 Hom.: 541

Bravo AF: 0.165

Asia WGS AF: 0.0360 AC: 126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.6
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6744978; hg19: chr2-192053706;