rs1605209

Variant names:

• chr4-33397412-G-A
• rs1605209
• ENST00000823071.1:n.231-6267C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-33397412-G-A
• chr4-33397412-G-C
• chr4-33397412-G-T

Variant summary

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

The ENST00000823071.1(ENSG00000307042):​n.231-6267C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.072 in 152,110 control chromosomes in the GnomAD database, including 706 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 0.072 (706 hom., cov: 32)
• Consequence: ENSG00000307042 ENST00000823071.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 0 publications found

Genes affected

ENSG00000307042 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000823071.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307042	ENST00000823071.1		n.231-6267C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0715 AC: 10875 AN: 151992 Hom.: 683 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0277

Gnomad EAS AF: 0.0872

Gnomad SAS AF: 0.0959

Gnomad FIN AF: 0.0341

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0185

Gnomad OTH AF: 0.0666

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

GnomAD4 genome AF: 0.0720 AC: 10948 AN: 152110 Hom.: 706 Cov.: 32 AF XY: 0.0736 AC XY: 5477 AN XY: 74370

African (AFR) AF: 0.156 AC: 6451 AN: 41478

American (AMR) AF: 0.105 AC: 1600 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0277 AC: 96 AN: 3470

East Asian (EAS) AF: 0.0870 AC: 449 AN: 5158

South Asian (SAS) AF: 0.0957 AC: 462 AN: 4826

European-Finnish (FIN) AF: 0.0341 AC: 361 AN: 10582

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0185 AC: 1259 AN: 67988

Other (OTH) AF: 0.0758 AC: 160 AN: 2110

Alfa AF: 0.0251 Hom.: 33

Bravo AF: 0.0836

Asia WGS AF: 0.134 AC: 465 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.61
PhyloP100		0.36

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1605209;

hg19: chr4-33399034;