7-107859502-T-C

Position:

• chr7-107859502-T-C

Variant summary

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

The XR_927850.3(LOC105375444):​n.105-2386A>G 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 0.522 in 152,066 control chromosomes in the GnomAD database, including 22,160 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 0.52 (22160 hom., cov: 32)
• Consequence: LOC105375444 XR_927850.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178

Genes affected

LOC105375444 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375444	XR_927850.3	n.105-2386A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79315 AN: 151950 Hom.: 22153 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.723

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.856

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.522 AC: 79329 AN: 152066 Hom.: 22160 Cov.: 32 AF XY: 0.531 AC XY: 39442 AN XY: 74328

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.615

Gnomad4 EAS AF: 0.855

Gnomad4 SAS AF: 0.573

Gnomad4 FIN AF: 0.604

Gnomad4 NFE AF: 0.583

Gnomad4 OTH AF: 0.548

Alfa AF: 0.534 Hom.: 7653

Bravo AF: 0.509

Asia WGS AF: 0.719 AC: 2500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6947045; hg19: chr7-107499947;