rs7548070

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr1-196923192-G-A
• chr1-196923192-G-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371675	XR_007066779.1	n.258-181C>T		intron_variant	Intron 1 of 2

Ensembl

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

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 v4.3

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;