rs61768478

Variant names:

• chr1-1161911-C-A
• rs61768478
• XR_007065350.1:n.2419C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-1161911-C-A
• chr1-1161911-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007065350.1(LOC124903820):​n.2419C>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 0.234 in 152,200 control chromosomes in the GnomAD database, including 4,630 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 0.23 (4630 hom., cov: 35)
• Consequence: LOC124903820 XR_007065350.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.66
• Publications: 3 publications found

Genes affected

LOC124903820 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903820	XR_007065350.1	n.2419C>A		non_coding_transcript_exon_variant	Exon 2 of 2
LOC124903820	XR_007065351.1	n.1701C>A		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35602 AN: 152082 Hom.: 4629 Cov.: 35

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.0515

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.234 AC: 35619 AN: 152200 Hom.: 4630 Cov.: 35 AF XY: 0.233 AC XY: 17311 AN XY: 74430

African (AFR) AF: 0.181 AC: 7514 AN: 41538

American (AMR) AF: 0.152 AC: 2319 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 704 AN: 3472

East Asian (EAS) AF: 0.0514 AC: 266 AN: 5176

South Asian (SAS) AF: 0.201 AC: 971 AN: 4824

European-Finnish (FIN) AF: 0.320 AC: 3392 AN: 10596

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19677 AN: 67976

Other (OTH) AF: 0.214 AC: 452 AN: 2114

Alfa AF: 0.175 Hom.: 400

Bravo AF: 0.216

Asia WGS AF: 0.111 AC: 387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.0060
DANN	Benign	0.68
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs61768478; hg19: chr1-1097291;