rs16836421

Variant names:

• chr1-238137437-A-G
• rs16836421
• ENST00000780747.1:n.360+20773A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-238137437-A-G
• chr1-238137437-A-T

Variant summary

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

The ENST00000780747.1(ENSG00000301680):​n.360+20773A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0466 in 151,642 control chromosomes in the GnomAD database, including 196 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 0.047 (196 hom., cov: 30)
• Consequence: ENSG00000301680 ENST00000780747.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319
• Publications: 1 publications found

Genes affected

ENSG00000301680 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0926 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000780747.1. 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
	ENSG00000301680	ENST00000780747.1		n.360+20773A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0466 AC: 7066 AN: 151530 Hom.: 196 Cov.: 30

Gnomad AFR AF: 0.0550

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0313

Gnomad ASJ AF: 0.0889

Gnomad EAS AF: 0.0363

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0282

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0430

Gnomad OTH AF: 0.0491

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

GnomAD4 genome AF: 0.0466 AC: 7074 AN: 151642 Hom.: 196 Cov.: 30 AF XY: 0.0462 AC XY: 3425 AN XY: 74128

African (AFR) AF: 0.0553 AC: 2286 AN: 41356

American (AMR) AF: 0.0313 AC: 477 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0889 AC: 308 AN: 3464

East Asian (EAS) AF: 0.0362 AC: 186 AN: 5136

South Asian (SAS) AF: 0.100 AC: 478 AN: 4782

European-Finnish (FIN) AF: 0.0282 AC: 296 AN: 10480

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0430 AC: 2920 AN: 67868

Other (OTH) AF: 0.0500 AC: 105 AN: 2100

Alfa AF: 0.0459 Hom.: 203

Bravo AF: 0.0456

Asia WGS AF: 0.0930 AC: 321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	7.6
DANN	Benign	0.72
PhyloP100		0.32

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: rs16836421;

hg19: chr1-238300737;

COSMIC: COSV60041984;