rs61822012

Variant names:

• chr1-160071368-A-G
• rs61822012
• ENST00000435580.2:n.434+6337A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-160071368-A-G
• chr1-160071368-A-T

Variant summary

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

The ENST00000435580.2(ENSG00000225279):​n.434+6337A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 152,246 control chromosomes in the GnomAD database, including 4,547 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 0.22 (4547 hom., cov: 33)
• Consequence: ENSG00000225279 ENST00000435580.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158

Genes affected

ENSG00000225279 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000225279	ENST00000435580.2	n.434+6337A>G		intron_variant	Intron 4 of 4	3
ENSG00000225279	ENST00000662080.1	n.238+6451A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33436 AN: 152128 Hom.: 4549 Cov.: 33

Gnomad AFR AF: 0.0594

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.220 AC: 33434 AN: 152246 Hom.: 4547 Cov.: 33 AF XY: 0.220 AC XY: 16388 AN XY: 74444

Gnomad4 AFR AF: 0.0593

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.210

Alfa AF: 0.236 Hom.: 585

Bravo AF: 0.204

Asia WGS AF: 0.193 AC: 672 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.8
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs61822012; hg19: chr1-160041158;