7-148422604-G-A

Position:

• chr7-148422604-G-A

Variant summary

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

The XR_928094.2(LOC105375554):​n.209+13955C>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 0.192 in 151,964 control chromosomes in the GnomAD database, including 4,988 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 0.19 (4988 hom., cov: 32)
• Consequence: LOC105375554 XR_928094.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

LOC105375554 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375554	XR_928094.2	n.209+13955C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29128 AN: 151846 Hom.: 4983 Cov.: 32

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.0582

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0848

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.0915

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.192 AC: 29162 AN: 151964 Hom.: 4988 Cov.: 32 AF XY: 0.187 AC XY: 13923 AN XY: 74306

Gnomad4 AFR AF: 0.464

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.100

Gnomad4 FIN AF: 0.0848

Gnomad4 NFE AF: 0.0914

Gnomad4 OTH AF: 0.166

Alfa AF: 0.103 Hom.: 812

Bravo AF: 0.205

Asia WGS AF: 0.0730 AC: 254 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10229692; hg19: chr7-148119696;