chr1-159706221-G-A

Variant names:

• chr1-159706221-G-A
• rs2808628
• ENST00000751816.1:n.108-20306G>A

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.108-20306G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 152,040 control chromosomes in the GnomAD database, including 8,111 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 0.32 (8111 hom., cov: 32)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.259
• Publications: 18 publications found

Genes affected

ENSG00000297913 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751816.1. 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
	ENSG00000297913	ENST00000751816.1		n.108-20306G>A		intron	N/A
	ENSG00000297913	ENST00000751817.1		n.110-20306G>A		intron	N/A
	ENSG00000297913	ENST00000751818.1		n.63-20306G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.316 AC: 47994 AN: 151922 Hom.: 8103 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.316 AC: 48018 AN: 152040 Hom.: 8111 Cov.: 32 AF XY: 0.320 AC XY: 23788 AN XY: 74296

African (AFR) AF: 0.213 AC: 8854 AN: 41488

American (AMR) AF: 0.373 AC: 5699 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1241 AN: 3472

East Asian (EAS) AF: 0.582 AC: 3006 AN: 5162

South Asian (SAS) AF: 0.312 AC: 1507 AN: 4824

European-Finnish (FIN) AF: 0.375 AC: 3957 AN: 10548

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22752 AN: 67970

Other (OTH) AF: 0.333 AC: 703 AN: 2112

Alfa AF: 0.317 Hom.: 10535

Bravo AF: 0.311

Asia WGS AF: 0.440 AC: 1529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.8
DANN	Benign	0.78
PhyloP100		0.26

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: rs2808628;

hg19: chr1-159676011;