rs3761955

Positions:

• chr1-94543099-G-A
• chr1-94543099-G-C

Variant summary

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

The XR_007066234.1(LOC124904223):​n.1126G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 152,054 control chromosomes in the GnomAD database, including 12,042 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 (12042 hom., cov: 33)
• Consequence: LOC124904223 XR_007066234.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.848

Genes affected

LOC124904223 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904223	XR_007066234.1	n.1126G>A		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000702722.1	n.154+1006G>A		intron_variant, non_coding_transcript_variant
	ENST00000689973.2	n.1163G>A		non_coding_transcript_exon_variant	1/1
	ENST00000690992.2	n.914-106G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58266 AN: 151936 Hom.: 12040 Cov.: 33

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.383 AC: 58298 AN: 152054 Hom.: 12042 Cov.: 33 AF XY: 0.379 AC XY: 28124 AN XY: 74290

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.437

Alfa AF: 0.414 Hom.: 2195

Bravo AF: 0.385

Asia WGS AF: 0.275 AC: 959 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	11
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: rs3761955; hg19: chr1-95008655;