chr1-160399582-T-G

Variant names:

• chr1-160399582-T-G
• rs11582932
• XR_007066686.1:n.481+6590A>C

Variant summary

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

The XR_007066686.1(LOC105371466):​n.481+6590A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,084 control chromosomes in the GnomAD database, including 9,122 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 0.34 (9122 hom., cov: 32)
• Consequence: LOC105371466 XR_007066686.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.716
• Publications: 14 publications found

Genes affected

LOC105371466 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371466	XR_007066686.1	n.481+6590A>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51979 AN: 151966 Hom.: 9124 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.342 AC: 52014 AN: 152084 Hom.: 9122 Cov.: 32 AF XY: 0.341 AC XY: 25369 AN XY: 74324

African (AFR) AF: 0.321 AC: 13301 AN: 41462

American (AMR) AF: 0.379 AC: 5786 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 978 AN: 3466

East Asian (EAS) AF: 0.278 AC: 1446 AN: 5194

South Asian (SAS) AF: 0.486 AC: 2342 AN: 4818

European-Finnish (FIN) AF: 0.277 AC: 2931 AN: 10576

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.353 AC: 24012 AN: 67978

Other (OTH) AF: 0.346 AC: 731 AN: 2112

Alfa AF: 0.355 Hom.: 16470

Bravo AF: 0.349

Asia WGS AF: 0.375 AC: 1304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.9
DANN	Benign	0.55
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs11582932; hg19: chr1-160369372;