chr1-108830979-C-T

Variant names:

• chr1-108830979-C-T
• rs10494100
• NM_152763.5:c.1747-329G>A

Variant summary

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

The NM_152763.5(AKNAD1):​c.1747-329G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,226 control chromosomes in the GnomAD database, including 2,023 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 0.15 (2023 hom., cov: 32)
• Consequence: AKNAD1 NM_152763.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.462
• Publications: 4 publications found

Genes affected

AKNAD1 (HGNC:28398): (AKNA domain containing 1) This gene encodes a protein which contains a domain found in an AT-hook-containing transcription factor. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2012]

LOC105378891 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AKNAD1	NM_152763.5	c.1747-329G>A		intron_variant	Intron 9 of 15	ENST00000370001.8	NP_689976.2
AKNAD1	NR_049760.2	n.1959-329G>A		intron_variant	Intron 8 of 13
LOC105378891	XR_007066273.1	n.148-3211C>T		intron_variant	Intron 2 of 4
LOC105378891	XR_947687.3	n.123-3211C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AKNAD1	ENST00000370001.8	c.1747-329G>A		intron_variant	Intron 9 of 15	1	NM_152763.5	ENSP00000359018.3

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22990 AN: 152108 Hom.: 2020 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.0681

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.0983

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.0862

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.151 AC: 23015 AN: 152226 Hom.: 2023 Cov.: 32 AF XY: 0.147 AC XY: 10974 AN XY: 74412

African (AFR) AF: 0.246 AC: 10209 AN: 41508

American (AMR) AF: 0.117 AC: 1784 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0983 AC: 341 AN: 3470

East Asian (EAS) AF: 0.113 AC: 588 AN: 5184

South Asian (SAS) AF: 0.0862 AC: 416 AN: 4824

European-Finnish (FIN) AF: 0.115 AC: 1214 AN: 10602

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8082 AN: 68022

Other (OTH) AF: 0.136 AC: 287 AN: 2114

Alfa AF: 0.108 Hom.: 518

Bravo AF: 0.154

Asia WGS AF: 0.108 AC: 376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.93
DANN	Benign	0.71
PhyloP100		-0.46
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: rs10494100; hg19: chr1-109373601;