rs1564505

Variant names:

• chr1-238253180-A-C
• rs1564505
• ENST00000422844.2:n.74+14168A>C

Your query was ambiguous. Multiple possible variants found:

• chr1-238253180-A-C
• chr1-238253180-A-G

Variant summary

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

The ENST00000422844.2(ENSG00000234464):​n.74+14168A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 151,534 control chromosomes in the GnomAD database, including 27,561 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 0.60 (27561 hom., cov: 31)
• Consequence: ENSG00000234464 ENST00000422844.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 1 publications found

Genes affected

ENSG00000234464 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000422844.2. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000234464	ENST00000422844.2	TSL:3	n.74+14168A>C		intron	N/A
	ENSG00000234464	ENST00000665394.1		n.70+14168A>C		intron	N/A
	ENSG00000234464	ENST00000716147.1		n.245+1632A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.600 AC: 90875 AN: 151414 Hom.: 27533 Cov.: 31

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.539

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.600 AC: 90950 AN: 151534 Hom.: 27561 Cov.: 31 AF XY: 0.608 AC XY: 45002 AN XY: 74036

African (AFR) AF: 0.553 AC: 22843 AN: 41328

American (AMR) AF: 0.703 AC: 10720 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.648 AC: 2246 AN: 3466

East Asian (EAS) AF: 0.700 AC: 3568 AN: 5096

South Asian (SAS) AF: 0.588 AC: 2825 AN: 4802

European-Finnish (FIN) AF: 0.681 AC: 7152 AN: 10502

Middle Eastern (MID) AF: 0.538 AC: 155 AN: 288

European-Non Finnish (NFE) AF: 0.585 AC: 39679 AN: 67800

Other (OTH) AF: 0.592 AC: 1250 AN: 2110

Alfa AF: 0.600 Hom.: 3570

Bravo AF: 0.606

Asia WGS AF: 0.645 AC: 2237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.72
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1564505; hg19: chr1-238416480;