rs61822012

chr1-160071368-A-Gchr1-160071368-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, non coding transcript 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: ENST00000435580.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000435580.2	n.434+6337A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000662080.1	n.238+6451A>G		intron_variant, non_coding_transcript_variant

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;