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. The variant received -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
• Publications: 3 publications found

Genes affected

ENSG00000225279 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435580.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000225279	ENST00000435580.2	TSL:3	n.434+6337A>G		intron	N/A
	ENSG00000225279	ENST00000662080.1		n.238+6451A>G		intron	N/A
	ENSG00000225279	ENST00000772467.1		n.55+2042A>G		intron	N/A

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

African (AFR) AF: 0.0593 AC: 2463 AN: 41552

American (AMR) AF: 0.216 AC: 3296 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.292 AC: 1015 AN: 3472

East Asian (EAS) AF: 0.225 AC: 1166 AN: 5176

South Asian (SAS) AF: 0.202 AC: 976 AN: 4824

European-Finnish (FIN) AF: 0.344 AC: 3643 AN: 10602

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20201 AN: 68010

Other (OTH) AF: 0.210 AC: 443 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.8
DANN	Benign	0.44
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs61822012; hg19: chr1-160041158;