rs7548070

Positions:

• chr1-196923192-G-A
• chr1-196923192-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007066779.1(LOC105371675):​n.258-181C>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.428

Genes affected

LOC105371675 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC105371675	XR_007066779.1	n.258-181C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.000775

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.0928

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.178

Alfa AF: 0.128 Hom.: 1024

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs7548070; hg19: chr1-196892322;