1-196923192-G-A

Variant names:

• chr1-196923192-G-A
• rs7548070
• XR_007066779.1:n.258-181C>T

Variant summary

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

The XR_007066779.1(LOC105371675):​n.258-181C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 151,264 control chromosomes in the GnomAD database, including 2,855 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 0.17 (2855 hom., cov: 32)
• Consequence: LOC105371675 XR_007066779.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.428
• Publications: 5 publications found

Genes affected

LOC105371675 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25271 AN: 151148 Hom.: 2854 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.000773

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0928

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.167 AC: 25281 AN: 151264 Hom.: 2855 Cov.: 32 AF XY: 0.165 AC XY: 12183 AN XY: 73922

African (AFR) AF: 0.284 AC: 11619 AN: 40924

American (AMR) AF: 0.127 AC: 1923 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 405 AN: 3466

East Asian (EAS) AF: 0.000775 AC: 4 AN: 5162

South Asian (SAS) AF: 0.144 AC: 692 AN: 4800

European-Finnish (FIN) AF: 0.0928 AC: 977 AN: 10530

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9136 AN: 67920

Other (OTH) AF: 0.178 AC: 374 AN: 2098

Alfa AF: 0.135 Hom.: 1498

Bravo AF: 0.173

Asia WGS AF: 0.0780 AC: 272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.9
DANN	Benign	0.35
PhyloP100		0.43
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: rs7548070; hg19: chr1-196892322;