rs999917

Variant names:

• chr1-39006034-T-A
• rs999917
• NM_024595.3:c.*1979T>A

Variant summary

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

The NM_024595.3(AKIRIN1):​c.*1979T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 151,924 control chromosomes in the GnomAD database, including 7,509 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 0.27 (7509 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: AKIRIN1 NM_024595.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.00
• Publications: 9 publications found

Genes affected

AKIRIN1 (HGNC:25744): (akirin 1) Predicted to enable transcription coregulator activity. Predicted to be involved in several processes, including myoblast migration involved in skeletal muscle regeneration; negative regulation of satellite cell differentiation; and positive regulation of lamellipodium assembly. Located in nuclear membrane and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AKIRIN1	NM_024595.3	c.*1979T>A		3_prime_UTR_variant	Exon 5 of 5	ENST00000432648.8	NP_078871.1
AKIRIN1	NM_001136275.2	c.*1979T>A		3_prime_UTR_variant	Exon 4 of 4		NP_001129747.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AKIRIN1	ENST00000432648.8	c.*1979T>A		3_prime_UTR_variant	Exon 5 of 5	1	NM_024595.3	ENSP00000392678.3

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41688 AN: 151806 Hom.: 7509 Cov.: 32

Gnomad AFR AF: 0.0712

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.298

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.274 AC: 41682 AN: 151924 Hom.: 7509 Cov.: 32 AF XY: 0.272 AC XY: 20224 AN XY: 74232

African (AFR) AF: 0.0710 AC: 2948 AN: 41532

American (AMR) AF: 0.256 AC: 3894 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1349 AN: 3468

East Asian (EAS) AF: 0.119 AC: 615 AN: 5176

South Asian (SAS) AF: 0.131 AC: 632 AN: 4818

European-Finnish (FIN) AF: 0.452 AC: 4733 AN: 10470

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26640 AN: 67912

Other (OTH) AF: 0.294 AC: 620 AN: 2106

Alfa AF: 0.313 Hom.: 1072

Bravo AF: 0.254

Asia WGS AF: 0.104 AC: 361 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	7.1
DANN	Benign	0.63
PhyloP100		3.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs999917; hg19: chr1-39471706;