rs164041

Variant names:

• chr1-162378327-G-C
• rs164041
• ENST00000420220.1:c.-11-3564G>C

Variant summary

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

The ENST00000420220.1(ENSG00000254706):​c.-11-3564G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,208 control chromosomes in the GnomAD database, including 1,792 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 0.14 (1792 hom., cov: 32)
• Consequence: ENSG00000254706 ENST00000420220.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.309

Genes affected

ENSG00000254706 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.181 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
ENSG00000254706	ENST00000420220.1	c.-11-3564G>C		intron_variant	Intron 2 of 3	5		ENSP00000398035.1
ENSG00000254706	ENST00000431696.1	c.227-3564G>C		intron_variant	Intron 2 of 2	4		ENSP00000405676.2
ENSG00000254706	ENST00000367932.3	n.153-3564G>C		intron_variant	Intron 1 of 2	4		ENSP00000356909.3

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21419 AN: 152090 Hom.: 1790 Cov.: 32

Gnomad AFR AF: 0.0564

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.0648

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.141 AC: 21425 AN: 152208 Hom.: 1792 Cov.: 32 AF XY: 0.140 AC XY: 10445 AN XY: 74422

Gnomad4 AFR AF: 0.0562

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.0645

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.184

Alfa AF: 0.174 Hom.: 335

Bravo AF: 0.133

Asia WGS AF: 0.126 AC: 437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.1
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs164041; hg19: chr1-162348117;